Isolated polynucleotides and polypeptides and methods of using same for increasing plant yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance of plants and nitrogen use efficiency

ABSTRACT

Provided are isolated polynucleotides encoding a polypeptide at least 80% homologous to the amino acid sequence selected from the group consisting of SEQ ID NOs: 757, 456-756, 758-774, 8385-10836, and 10838-14462; and isolated polynucleotide comprising nucleic acid sequences at least 80% identical to SEQ ID NO: 377, 1-376, 378-455, and 775-8384. Also provided are nucleic acid constructs comprising same, isolated polypeptides encoded thereby, transgenic cells and transgenic plants comprising same and methods of using same for increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of a plant.

RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No. 14/115,397 filed on Nov. 4, 2013 which is a National Phase of PCT Patent Application No. PCT/IL2012/050154 having International filing date of May 2, 2012, which claims the benefit of priority under 35 USC § 119(e) of U.S. Provisional Patent Application No. 61/481,752 filed on May 3, 2011 and 61/537,621 filed on Sep. 22, 2011.

The contents of the above applications are all incorporated by reference as if fully set forth herein in their entirety.

SEQUENCE LISTING STATEMENT

The ASCII file, entitled 76075SequenceListing.txt, created on Dec. 10, 2018, comprising 33,138,135 bytes, submitted concurrently with the filing of this application is incorporated herein by reference.

FIELD AND BACKGROUND OF THE INVENTION

The present invention, in some embodiments thereof, relates to isolated polypeptides and polynucleotides, nucleic acid constructs comprising same, transgenic cells comprising same, transgenic plants exogenously expressing same and more particularly, but not exclusively, to methods of using same for increasing yield (e.g., seed yield, oil yield), biomass, growth rate, vigor, oil content, fiber yield, fiber quality abiotic stress tolerance, and/or fertilizer use efficiency (e.g., nitrogen use efficiency) of a plant.

A common approach to promote plant growth has been, and continues to be, the use of natural as well as synthetic nutrients (fertilizers). Thus, fertilizers are the fuel behind the “green revolution”, directly responsible for the exceptional increase in crop yields during the last 40 years, and are considered the number one overhead expense in agriculture. Of the three macronutrients provided as main fertilizers [Nitrogen (N), Phosphate (P) and Potassium (K)], nitrogen is often the rate-limiting element in plant growth and all field crops have a fundamental dependence on inorganic nitrogenous fertilizer. Nitrogen usually needs to be replenished every year, particularly for cereals, which comprise more than half of the cultivated areas worldwide. For example, inorganic nitrogenous fertilizers such as ammonium nitrate, potassium nitrate, or urea, typically accounts for 40% of the costs associated with crops such as corn and wheat.

Nitrogen is an essential macronutrient for the plant, responsible for biosynthesis of amino and nucleic acids, prosthetic groups, plant hormones, plant chemical defenses, etc. In addition, nitrogen is often the rate-limiting element in plant growth and all field crops have a fundamental dependence on inorganic nitrogen. Thus, nitrogen is translocated to the shoot, where it is stored in the leaves and stalk during the rapid step of plant development and up until flowering. In corn for example, plants accumulate the bulk of their organic nitrogen during the period of grain germination, and until flowering. Once fertilization of the plant has occurred, grains begin to form and become the main sink of plant nitrogen. The stored nitrogen can be then redistributed from the leaves and stalk that served as storage compartments until grain formation.

Since fertilizer is rapidly depleted from most soil types, it must be supplied to growing crops two or three times during the growing season. In addition, the low nitrogen use efficiency (NUE) of the main crops (e.g., in the range of only 30-70%) negatively affects the input expenses for the farmer, due to the excess fertilizer applied. Moreover, the over and inefficient use of fertilizers are major factors responsible for environmental problems such as eutrophication of groundwater, lakes, rivers and seas, nitrate pollution in drinking water which can cause methemoglobinemia, phosphate pollution, atmospheric pollution and the like. However, in spite of the negative impact of fertilizers on the environment, and the limits on fertilizer use, which have been legislated in several countries, the use of fertilizers is expected to increase in order to support food and fiber production for rapid population growth on limited land resources.

For example, it has been estimated that by 2050, more than 150 million tons of nitrogenous fertilizer will be used worldwide annually.

Increased use efficiency of nitrogen by plants should enable crops to be cultivated with lower fertilizer input, or alternatively to be cultivated on soils of poorer quality and would therefore have significant economic impact in both developed and developing agricultural systems.

Genetic improvement of fertilizer use efficiency (FUE) in plants can be generated either via traditional breeding or via genetic engineering.

Attempts to generate plants with increased FUE have been described in U.S. Pat. Appl. No. 20020046419 to Choo, et al.; U.S. Pat. Appl. No. 20050108791 to Edgerton et al.; U.S. Pat. Appl. No. 20060179511 to Chomet et al.; Good, A, et al. 2007 (Engineering nitrogen use efficiency with alanine aminotransferase. Canadian Journal of Botany 85: 252-262); and Good A G et al. 2004 (Trends Plant Sci. 9:597-605).

Yanagisawa et al. (Proc. Natl. Acad. Sci. U.S.A. 2004 101:7833-8) describe Dofl transgenic plants which exhibit improved growth under low-nitrogen conditions.

U.S. Pat. No. 6,084,153 to Good et al. discloses the use of a stress responsive promoter to control the expression of Alanine Amine Transferase (AlaAT) and transgenic canola plants with improved drought and nitrogen deficiency tolerance when compared to control plants.

The ever-increasing world population and the decreasing availability in arable land for agriculture affect the yield of plants and plant-related products. The global shortage of water supply, desertification, abiotic stress (ABS) conditions (e.g., salinity, drought, flood, suboptimal temperature and toxic chemical pollution), and/or limited nitrogen and fertilizer sources cause substantial damage to agricultural plants such as major alterations in the plant metabolism, cell death, and decreases in plant growth and crop productivity.

Drought is a gradual phenomenon, which involves periods of abnormally dry weather that persists long enough to produce serious hydrologic imbalances such as crop damage, water supply shortage and increased susceptibility to various diseases.

Salinity, high salt levels, affects one in five hectares of irrigated land. None of the top five food crops, i.e., wheat, corn, rice, potatoes, and soybean, can tolerate excessive salt. Detrimental effects of salt on plants result from both water deficit, which leads to osmotic stress (similar to drought stress), and the effect of excess sodium ions on critical biochemical processes. As with freezing and drought, high salt causes water deficit; and the presence of high salt makes it difficult for plant roots to extract water from their environment. Thus, salination of soils that are used for agricultural production is a significant and increasing problem in regions that rely heavily on agriculture, and is worsen by over-utilization, over-fertilization and water shortage, typically caused by climatic change and the demands of increasing population.

Suboptimal temperatures affect plant growth and development through the whole plant life cycle. Thus, low temperatures reduce germination rate and high temperatures result in leaf necrosis. In addition, mature plants that are exposed to excess of heat may experience heat shock, which may arise in various organs, including leaves and particularly fruit, when transpiration is insufficient to overcome heat stress. Heat also damages cellular structures, including organelles and cytoskeleton, and impairs membrane function. Heat shock may produce a decrease in overall protein synthesis, accompanied by expression of heat shock proteins, e.g., chaperones, which are involved in refolding proteins denatured by heat. High-temperature damage to pollen almost always occurs in conjunction with drought stress, and rarely occurs under well-watered conditions. Combined stress can alter plant metabolism in novel ways. Excessive chilling conditions, e.g., low, but above freezing, temperatures affect crops of tropical origins, such as soybean, rice, maize, and cotton. Typical chilling damage includes wilting, necrosis, chlorosis or leakage of ions from cell membranes. Excessive light conditions, which occur under clear atmospheric conditions subsequent to cold late summer/autumn nights, can lead to photoinhibition of photosynthesis (disruption of photosynthesis). In addition, chilling may lead to yield losses and lower product quality through the delayed ripening of maize.

Nutrient deficiencies cause adaptations of the root architecture, particularly notably for example is the root proliferation within nutrient rich patches to increase nutrient uptake. Nutrient deficiencies cause also the activation of plant metabolic pathways which maximize the absorption, assimilation and distribution processes such as by activating architectural changes. Engineering the expression of the triggered genes may cause the plant to exhibit the architectural changes and enhanced metabolism also under other conditions.

In addition, it is widely known that the plants usually respond to water deficiency by creating a deeper root system that allows access to moisture located in deeper soil layers. Triggering this effect will allow the plants to access nutrients and water located in deeper soil horizons particularly those readily dissolved in water like nitrates.

Yield is affected by various factors, such as, the number and size of the plant organs, plant architecture (for example, the number of branches), grains set length, number of filled grains, vigor (e.g. seedling), growth rate, root development, utilization of water, nutrients (e.g., nitrogen) and fertilizers, and stress tolerance.

Crops such as, corn, rice, wheat, canola and soybean account for over half of total human caloric intake, whether through direct consumption of the seeds themselves or through consumption of meat products raised on processed seeds or forage. Seeds are also a source of sugars, proteins and oils and metabolites used in industrial processes. The ability to increase plant yield, whether through increase dry matter accumulation rate, modifying cellulose or lignin composition, increase stalk strength, enlarge meristem size, change of plant branching pattern, erectness of leaves, increase in fertilization efficiency, enhanced seed dry matter accumulation rate, modification of seed development, enhanced seed filling or by increasing the content of oil, starch or protein in the seeds would have many applications in agricultural and non-agricultural uses such as in the biotechnological production of pharmaceuticals, antibodies or vaccines.

Studies have shown that plant adaptations to adverse environmental conditions are complex genetic traits with polygenic nature. Conventional means for crop and horticultural improvements utilize selective breeding techniques to identify plants having desirable characteristics. However, selective breeding is tedious, time consuming and has an unpredictable outcome. Furthermore, limited germplasm resources for yield improvement and incompatibility in crosses between distantly related plant species represent significant problems encountered in conventional breeding. Advances in genetic engineering have allowed mankind to modify the germplasm of plants by expression of genes-of-interest in plants. Such a technology has the capacity to generate crops or plants with improved economic, agronomic or horticultural traits.

WO publication No. 2009/013750 discloses genes, constructs and methods of increasing abiotic stress tolerance, biomass and/or yield in plants generated thereby.

WO publication No. 2008/122980 discloses genes constructs and methods for increasing oil content, growth rate and biomass of plants.

WO publication No. 2008/075364 discloses polynucleotides involved in plant fiber development and methods of using same.

WO publication No. 2007/049275 discloses isolated polypeptides, polynucleotides encoding same, transgenic plants expressing same and methods of using same for increasing fertilizer use efficiency, plant abiotic stress tolerance and biomass.

WO publication No. 2004/104162 discloses methods of increasing abiotic stress tolerance and/or biomass in plants and plants generated thereby.

WO publication No. 2005/121364 discloses polynucleotides and polypeptides involved in plant fiber development and methods of using same for improving fiber quality, yield and/or biomass of a fiber producing plant.

WO publication No. 2007/020638 discloses methods of increasing abiotic stress tolerance and/or biomass in plants and plants generated thereby.

WO publication No. 2009/083958 discloses methods of increasing water use efficiency, fertilizer use efficiency, biotic/abiotic stress tolerance, yield and biomass in plant and plants generated thereby.

WO publication No. 2010/020941 discloses methods of increasing nitrogen use efficiency, abiotic stress tolerance, yield and biomass in plants and plants generated thereby.

WO publication No. 2009/141824 discloses isolated polynucleotides and methods using same for increasing plant utility.

WO publication No. 2010/076756 discloses isolated polynucleotides for increasing abiotic stress tolerance, yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, and/or nitrogen use efficiency of a plant.

WO publication No. 2004/081173 discloses novel plant derived regulatory sequences and constructs and methods of using such sequences for directing expression of exogenous polynucleotide sequences in plants.

WO publication No. 2010/049897 discloses isolated polynucleotides and polypeptides and methods of using same for increasing plant yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance of plants and nitrogen use efficiency.

WO publication No. 2004/111183 discloses nucleotide sequences for regulating gene expression in plant trichomes and constructs and methods utilizing same.

WO publication No. 2011/080674 discloses isolated polynucleotides and polypeptides and methods of using same for increasing plant yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance of plants and nitrogen use efficiency.

WO2010/100595 publication discloses isolated polynucleotides and polypeptides, and methods of using same for increasing plant yield and/or agricultural characteristics.

WO2011/015985 publication discloses polynucleotides and polypeptides for increasing desirable plant qualities.

WO2010/143138 publication discloses isolated polynucleotides and polypeptides, and methods of using same for increasing nitrogen use efficiency, fertilizer use efficiency, yield, growth rate, vigor, biomass, oil content, abiotic stress tolerance and/or water use efficiency.

SUMMARY OF THE INVENTION

According to an aspect of some embodiments of the present invention there is provided a method of increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least 80% identical to SEQ ID NO: 456-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 or 14462, thereby increasing the yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of the plant.

According to an aspect of some embodiments of the present invention there is provided a method of increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide selected from the group consisting of SEQ ID NOs:456-774, 8385-10836, 10838-14461 and 14462, thereby increasing the yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of the plant.

According to an aspect of some embodiments of the present invention there is provided a method of increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence at least 80% identical to SEQ ID NO: 1-455, 775-6485, 6487-6657, 6660-6664, 6666-6701, 6703-6745, 6748-6818, 6820-6821, 6824-6827, 6829-6881, 6883, 6885-8383 or 8384, thereby increasing the yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of the plant.

According to an aspect of some embodiments of the present invention there is provided a method of increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of a plant, comprising expressing within the plant an exogenous polynucleotide comprising the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455, 775-8383 and 8384, thereby increasing the yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of the plant.

According to an aspect of some embodiments of the present invention there is provided a method of increasing nitrogen use efficiency and/or oil content of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least 80% identical to SEQ ID NO: 10837, thereby increasing the nitrogen use efficiency and/or oil content of the plant.

According to an aspect of some embodiments of the present invention there is provided a method of increasing nitrogen use efficiency and/or oil content of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding the polypeptide set forth in SEQ ID NO:10837, thereby increasing the nitrogen use efficiency and/or oil content of the plant.

According to an aspect of some embodiments of the present invention there is provided an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises an amino acid sequence at least 80% homologous to the amino acid sequence set forth in SEQ ID NO: 456-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 or 14462, wherein the amino acid sequence is capable of increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of a plant.

According to an aspect of some embodiments of the present invention there is provided an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises the amino acid sequence selected from the group consisting of SEQ ID NOs:456-774, 8385-10836, 10838-14461 and 14462.

According to an aspect of some embodiments of the present invention there is provided an isolated polynucleotide comprising a nucleic acid sequence at least 80% identical to SEQ ID NO:1-455, 775-6485, 6487-6657, 6660-6664, 6666-6701, 6703-6745, 6748-6818, 6820-6821, 6824-6827, 6829-6881, 6883, 6885-8383, or 8384, wherein the nucleic acid sequence is capable of increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of a plant.

According to an aspect of some embodiments of the present invention there is provided an isolated polynucleotide comprising the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455, 775-8383 and 8384.

According to an aspect of some embodiments of the present invention there is provided a nucleic acid construct comprising the isolated polynucleotide of some embodiments of the invention, and a promoter for directing transcription of the nucleic acid sequence in a host cell.

According to an aspect of some embodiments of the present invention there is provided an isolated polypeptide comprising an amino acid sequence at least 80% homologous to SEQ ID NO: 456-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 or 14462, wherein the amino acid sequence is capable of increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of a plant.

According to an aspect of some embodiments of the present invention there is provided an isolated polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NOs: 456-774, 8385-10836, and 10838-14462.

According to an aspect of some embodiments of the present invention there is provided a plant cell exogenously expressing the polynucleotide of some embodiments of the invention, or the nucleic acid construct of some embodiments of the invention.

According to an aspect of some embodiments of the present invention there is provided a plant cell exogenously expressing the polypeptide of some embodiments of the invention.

According to an aspect of some embodiments of the present invention there is provided a transgenic plant comprising the nucleic acid construct of some embodiments of the invention.

According to an aspect of some embodiments of the present invention there is provided a method of generating a transgenic plant, comprising expressing the nucleic acid construct of some embodiments of the invention within the plant, thereby generating the transgenic plant.

According to some embodiments of the invention, the nucleic acid sequence encodes an amino acid sequence selected from the group consisting of SEQ ID NOs: 456-774, 8385-10836, and 10838-14462.

According to some embodiments of the invention, the nucleic acid sequence is selected from the group consisting of SEQ ID NOs: 1-455, and 775-8384.

According to some embodiments of the invention, the polynucleotide consists of the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455, and 775-8384.

According to some embodiments of the invention, the nucleic acid sequence encodes the amino acid sequence selected from the group consisting of SEQ ID NOs:456-774, 8385-10836, and 10838-14462.

According to some embodiments of the invention, the plant cell forms part of a plant.

According to some embodiments of the invention, the method further comprising growing the plant expressing the exogenous polynucleotide under the abiotic stress condition(s).

According to some embodiments of the invention, the method further comprising growing the plant expressing the exogenous polynucleotide under the nitrogen-limiting condition(s).

According to some embodiments of the invention, the abiotic stress is selected from the group consisting of salinity, drought, water deprivation, flood, etiolation, low temperature, high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency, nutrient excess, atmospheric pollution and UV irradiation.

According to some embodiments of the invention, the yield comprises seed yield or oil yield.

According to some embodiments of the invention, the promoter is heterologous to the isolated polynucleotide and/or to the host cell.

According to some embodiments of the invention, the method further comprising growing the plant expressing the exogenous polynucleotide under nitrogen-limiting conditions.

Unless otherwise defined, all technical and/or scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the invention, exemplary methods and/or materials are described below. In case of conflict, the patent specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be necessarily limiting.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

Some embodiments of the invention are herein described, by way of example only, with reference to the accompanying drawings. With specific reference now to the drawings in detail, it is stressed that the particulars shown are by way of example and for purposes of illustrative discussion of embodiments of the invention. In this regard, the description taken with the drawings makes apparent to those skilled in the art how embodiments of the invention may be practiced.

In the drawings:

FIG. 1 is a schematic illustration of the modified pGI binary plasmid containing the new At6669 promoter (SEQ ID NO: 14467) and the GUSintron (pQYN 6669) used for expressing the isolated polynucleotide sequences of the invention. RB—T-DNA right border; LB—T-DNA left border; MCS—Multiple cloning site; RE—any restriction enzyme; NOS pro=nopaline synthase promoter; NPT-II=neomycin phosphotransferase gene; NOS ter=nopaline synthase terminator; Poly-A signal (polyadenylation signal); GUSintron—the GUS reporter gene (coding sequence and intron). The isolated polynucleotide sequences of the invention were cloned into the vector while replacing the GUSintron reporter gene.

FIG. 2 is a schematic illustration of the modified pGI binary plasmid containing the new At6669 promoter (SEQ ID NO: 14467) (pQFN or pQFNc) used for expressing the isolated polynucleotide sequences of the invention. RB—T-DNA right border; LB-T-DNA left border; MCS—Multiple cloning site; RE—any restriction enzyme; NOS pro=nopaline synthase promoter; NPT-II=neomycin phosphotransferase gene; NOS ter=nopaline synthase terminator; Poly-A signal (polyadenylation signal); The isolated polynucleotide sequences of the invention were cloned into the MCS of the vector.

FIGS. 3A-3F are images depicting visualization of root development of transgenic plants exogenously expressing the polynucleotide of some embodiments of the invention when grown in transparent agar plates under normal (FIGS. 3A-3B), osmotic stress (15% PEG; FIGS. 3C-3D) or nitrogen-limiting (FIGS. 3E-3F) conditions. The different transgenes were grown in transparent agar plates for 17 days (7 days nursery and 10 days after transplanting). The plates were photographed every 3-4 days starting at day 1 after transplanting. FIG. 3A—An image of a photograph of plants taken following 10 after transplanting days on agar plates when grown under normal (standard) conditions. FIG. 3B—An image of root analysis of the plants shown in FIG. 3A in which the lengths of the roots measured are represented by arrows. FIG. 3C—An image of a photograph of plants taken following 10 days after transplanting on agar plates, grown under high osmotic (PEG 15%) conditions. FIG. 3D—An image of root analysis of the plants shown in FIG. 3C in which the lengths of the roots measured are represented by arrows. FIG. 3E—An image of a photograph of plants taken following 10 days after transplanting on agar plates, grown under low nitrogen conditions. FIG. 3F—An image of root analysis of the plants shown in FIG. 3E in which the lengths of the roots measured are represented by arrows.

FIG. 4 is a schematic illustration of the modified pGI binary plasmid containing the Root Promoter (pQNa RP) used for expressing the isolated polynucleotide sequences of the invention. RB—T-DNA right border; LB—T-DNA left border; NOS pro=nopaline synthase promoter; NPT-II=neomycin phosphotransferase gene; NOS ter=nopaline synthase terminator; Poly-A signal (polyadenylation signal); The isolated polynucleotide sequences according to some embodiments of the invention were cloned into the MCS (Multiple cloning site) of the vector.

FIG. 5 is a schematic illustration of the pQYN plasmid.

FIG. 6 is a schematic illustration of the pQFN plasmid.

FIG. 7 is a schematic illustration of the pQFYN plasmid.

FIG. 8 is a schematic illustration of the modified pGI binary plasmid (pQXNc) used for expressing the isolated polynucleotide sequences of some embodiments of the invention. RB—T-DNA right border; LB—T-DNA left border; NOS pro=nopaline synthase promoter; NPT-II=neomycin phosphotransferase gene; NOS ter=nopaline synthase terminator; RE=any restriction enzyme; Poly-A signal (polyadenylation signal); 35S—the 35S promoter (SEQ ID NO: 14463). The isolated polynucleotide sequences of some embodiments of the invention were cloned into the MCS (Multiple cloning site) of the vector.

DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION

The present invention, in some embodiments thereof, relates to isolated polynucleotides and polypeptides, nucleic acid constructs encoding same, cells expressing same, transgenic plants expressing same and methods of using same for increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of a plant.

Before explaining at least one embodiment of the invention in detail, it is to be understood that the invention is not necessarily limited in its application to the details set forth in the following description or exemplified by the Examples. The invention is capable of other embodiments or of being practiced or carried out in various ways.

The present inventors have identified novel polypeptides and polynucleotides which can be used to increase yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality abiotic stress tolerance, and/or fertilizer use efficiency (e.g., nitrogen use efficiency) of a plant.

Thus, as shown in the Examples section which follows, the present inventors have utilized bioinformatics tools to identify polynucleotides which enhance yield (e.g., seed yield, oil yield, oil content), growth rate, biomass, vigor, fiber yield, fiber quality, abiotic stress tolerance and/or nitrogen use efficiency) of a plant. Genes which affect the trait-of-interest were identified [Table 53, Example 12, SEQ ID NOs: 1-455 (polynucleotides) and SEQ ID NOs: 456-774 (polypeptides)] based on correlation analyses performed using Arabidopsis ecotypes (Examples 2 and 3), tomato varieties (Example 4), b. Juncea ecotypes (Examples 5 and 6), Sorghum varieties (Example 7), Maize hybrids (Example 8), Soybean varieties (Example 9), Barley accessions (Example 10) and Cotton species (Examples 11) and the expression profiles of the genes according to selected expression sets (e.g., tissues, developmental stages and stress conditions) (Tables 1-53, Examples 1-12). Homologous polypeptides and polynucleotides having the same function were also identified [Table 54, Example 13; SEQ ID NOs: 775-8384 (polynucleotides) and SEQ ID NOs: 8385-14462 (polypeptides)]. The identified polynucleotides were cloned into binary vectors (Example 14) and transgenic plants over-expressing the identified polynucleotides and polypeptides were generated (Example 15) and further evaluated for the effect of the exogenous gene on the trait of interest (e.g., increased fresh and dry weight, leaf area, root coverage and length, relative growth rate (RGR) of leaf area, RGR of root coverage, RGR of root length, seed yield, oil yield, dry matter, harvest index, growth rate, rosette area, rosette diameter, RGR leaf number, RGR plot coverage, RGR rosette diameter, leaf blade area, oil percentage in seed and weight of 1000 seeds, plot coverage, tolerance to abiotic stress conditions and to fertilizer limiting conditions; Examples 16-18). Altogether, these results suggest the use of the novel polynucleotides and polypeptides of the invention for increasing yield (including oil yield, seed yield and oil content), growth rate, biomass, vigor, fiber yield, fiber quality, abiotic stress tolerance and/or nitrogen use efficiency of a plant.

Thus, according to an aspect of some embodiments of the invention, there is provided method of increasing yield, growth rate, biomass, vigor, oil content, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% homologous to the amino acid sequence selected from the group consisting of SEQ ID NOs: 456-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 and 14462, thereby increasing the yield, growth rate, biomass, vigor, oil content, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of the plant.

As used herein the phrase “plant yield” refers to the amount (e.g., as determined by weight or size) or quantity (numbers) of tissues or organs produced per plant or per growing season. Hence increased yield could affect the economic benefit one can obtain from the plant in a certain growing area and/or growing time.

It should be noted that a plant yield can be affected by various parameters including, but not limited to, plant biomass; plant vigor; growth rate; seed yield; seed or grain quantity; seed or grain quality; oil yield; content of oil, starch and/or protein in harvested organs (e.g., seeds or vegetative parts of the plant); number of flowers (florets) per panicle (expressed as a ratio of number of filled seeds over number of primary panicles); harvest index; number of plants grown per area; number and size of harvested organs per plant and per area; number of plants per growing area (density); number of harvested organs in field; total leaf area; carbon assimilation and carbon partitioning (the distribution/allocation of carbon within the plant); resistance to shade; number of harvestable organs (e.g. seeds), seeds per pod, weight per seed; and modified architecture [such as increase stalk diameter, thickness or improvement of physical properties (e.g. elasticity)].

As used herein the phrase “seed yield” refers to the number or weight of the seeds per plant, seeds per pod, or per growing area or to the weight of a single seed, or to the oil extracted per seed. Hence seed yield can be affected by seed dimensions (e.g., length, width, perimeter, area and/or volume), number of (filled) seeds and seed filling rate and by seed oil content. Hence increase seed yield per plant could affect the economic benefit one can obtain from the plant in a certain growing area and/or growing time; and increase seed yield per growing area could be achieved by increasing seed yield per plant, and/or by increasing number of plants grown on the same given area.

The term “seed” (also referred to as “grain” or “kernel”) as used herein refers to a small embryonic plant enclosed in a covering called the seed coat (usually with some stored food), the product of the ripened ovule of gymnosperm and angiosperm plants which occurs after fertilization and some growth within the mother plant.

The phrase “oil content” as used herein refers to the amount of lipids in a given plant organ, either the seeds (seed oil content) or the vegetative portion of the plant (vegetative oil content) and is typically expressed as percentage of dry weight (10% humidity of seeds) or wet weight (for vegetative portion).

It should be noted that oil content is affected by intrinsic oil production of a tissue (e.g., seed, vegetative portion), as well as the mass or size of the oil-producing tissue per plant or per growth period.

In one embodiment, increase in oil content of the plant can be achieved by increasing the size/mass of a plant's tissue(s) which comprise oil per growth period. Thus, increased oil content of a plant can be achieved by increasing the yield, growth rate, biomass and vigor of the plant.

As used herein the phrase “plant biomass” refers to the amount (e.g., measured in grams of air-dry tissue) of a tissue produced from the plant in a growing season, which could also determine or affect the plant yield or the yield per growing area. An increase in plant biomass can be in the whole plant or in parts thereof such as aboveground (harvestable) parts, vegetative biomass, roots and seeds.

As used herein the phrase “growth rate” refers to the increase in plant organ/tissue size per time (can be measured in cm² per day).

As used herein the phrase “plant vigor” refers to the amount (measured by weight) of tissue produced by the plant in a given time. Hence increased vigor could determine or affect the plant yield or the yield per growing time or growing area. In addition, early vigor (seed and/or seedling) results in improved field stand.

Improving early vigor is an important objective of modern rice breeding programs in both temperate and tropical rice cultivars. Long roots are important for proper soil anchorage in water-seeded rice. Where rice is sown directly into flooded fields, and where plants must emerge rapidly through water, longer shoots are associated with vigor. Where drill-seeding is practiced, longer mesocotyls and coleoptiles are important for good seedling emergence. The ability to engineer early vigor into plants would be of great importance in agriculture. For example, poor early vigor has been a limitation to the introduction of maize (Zea mays L.) hybrids based on Corn Belt germplasm in the European Atlantic.

It should be noted that a plant yield can be determined under stress (e.g., abiotic stress, nitrogen-limiting conditions) and/or non-stress (normal) conditions.

As used herein, the phrase “non-stress conditions” refers to the growth conditions (e.g., water, temperature, light-dark cycles, humidity, salt concentration, fertilizer concentration in soil, nutrient supply such as nitrogen, phosphorous and/or potassium), that do not significantly go beyond the everyday climatic and other abiotic conditions that plants may encounter, and which allow optimal growth, metabolism, reproduction and/or viability of a plant at any stage in its life cycle (e.g., in a crop plant from seed to a mature plant and back to seed again). Persons skilled in the art are aware of normal soil conditions and climatic conditions for a given plant in a given geographic location. It should be noted that while the non-stress conditions may include some mild variations from the optimal conditions (which vary from one type/species of a plant to another), such variations do not cause the plant to cease growing without the capacity to resume growth.

The phrase “abiotic stress” as used herein refers to any adverse effect on metabolism, growth, reproduction and/or viability of a plant. Accordingly, abiotic stress can be induced by suboptimal environmental growth conditions such as, for example, salinity, water deprivation, flooding, freezing, low or high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency, atmospheric pollution or UV irradiation. The implications of abiotic stress are discussed in the Background section.

The phrase “abiotic stress tolerance” as used herein refers to the ability of a plant to endure an abiotic stress without suffering a substantial alteration in metabolism, growth, productivity and/or viability.

Plants are subject to a range of environmental challenges. Several of these, including salt stress, general osmotic stress, drought stress and freezing stress, have the ability to impact whole plant and cellular water availability. Not surprisingly, then, plant responses to this collection of stresses are related. Zhu (2002) Ann. Rev. Plant Biol. 53: 247-273 et al. note that “most studies on water stress signaling have focused on salt stress primarily because plant responses to salt and drought are closely related and the mechanisms overlap”. Many examples of similar responses and pathways to this set of stresses have been documented. For example, the CBF transcription factors have been shown to condition resistance to salt, freezing and drought (Kasuga et al. (1999) Nature Biotech. 17: 287-291). The Arabidopsis rd29B gene is induced in response to both salt and dehydration stress, a process that is mediated largely through an ABA signal transduction process (Uno et al. (2000) Proc. Natl. Acad. Sci. USA 97: 11632-11637), resulting in altered activity of transcription factors that bind to an upstream element within the rd29B promoter. In Mesembryanthemum crystallinum (ice plant), Patharker and Cushman have shown that a calcium-dependent protein kinase (McCDPK1) is induced by exposure to both drought and salt stresses (Patharker and Cushman (2000) Plant J. 24: 679-691). The stress-induced kinase was also shown to phosphorylate a transcription factor, presumably altering its activity, although transcript levels of the target transcription factor are not altered in response to salt or drought stress. Similarly, Saijo et al. demonstrated that a rice salt/drought-induced calmodulin-dependent protein kinase (OsCDPK7) conferred increased salt and drought tolerance to rice when overexpressed (Saijo et al. (2000) Plant J. 23: 319-327).

Exposure to dehydration invokes similar survival strategies in plants as does freezing stress (see, for example, Yelenosky (1989) Plant Physiol 89: 444-451) and drought stress induces freezing tolerance (see, for example, Siminovitch et al. (1982) Plant Physiol 69: 250-255; and Guy et al. (1992) Planta 188: 265-270). In addition to the induction of cold-acclimation proteins, strategies that allow plants to survive in low water conditions may include, for example, reduced surface area, or surface oil or wax production. In another example increased solute content of the plant prevents evaporation and water loss due to heat, drought, salinity, osmoticum, and the like therefore providing a better plant tolerance to the above stresses.

It will be appreciated that some pathways involved in resistance to one stress (as described above), will also be involved in resistance to other stresses, regulated by the same or homologous genes. Of course, the overall resistance pathways are related, not identical, and therefore not all genes controlling resistance to one stress will control resistance to the other stresses. Nonetheless, if a gene conditions resistance to one of these stresses, it would be apparent to one skilled in the art to test for resistance to these related stresses. Methods of assessing stress resistance are further provided in the Examples section which follows.

As used herein the phrase “water use efficiency (WUE)” refers to the level of organic matter produced per unit of water consumed by the plant, i.e., the dry weight of a plant in relation to the plant's water use, e.g., the biomass produced per unit transpiration.

As used herein the phrase “fertilizer use efficiency” refers to the metabolic process(es) which lead to an increase in the plant's yield, biomass, vigor, and growth rate per fertilizer unit applied. The metabolic process can be the uptake, spread, absorbent, accumulation, relocation (within the plant) and use of one or more of the minerals and organic moieties absorbed by the plant, such as nitrogen, phosphates and/or potassium.

As used herein the phrase “fertilizer-limiting conditions” refers to growth conditions which include a level (e.g., concentration) of a fertilizer applied which is below the level needed for normal plant metabolism, growth, reproduction and/or viability.

As used herein the phrase “nitrogen use efficiency (NUE)” refers to the metabolic process(es) which lead to an increase in the plant's yield, biomass, vigor, and growth rate per nitrogen unit applied. The metabolic process can be the uptake, spread, absorbent, accumulation, relocation (within the plant) and use of nitrogen absorbed by the plant.

As used herein the phrase “nitrogen-limiting conditions” refers to growth conditions which include a level (e.g., concentration) of nitrogen (e.g., ammonium or nitrate) applied which is below the level needed for normal plant metabolism, growth, reproduction and/or viability.

Improved plant NUE and FUE is translated in the field into either harvesting similar quantities of yield, while implementing less fertilizers, or increased yields gained by implementing the same levels of fertilizers. Thus, improved NUE or FUE has a direct effect on plant yield in the field. Thus, the polynucleotides and polypeptides of some embodiments of the invention positively affect plant yield, seed yield, and plant biomass. In addition, the benefit of improved plant NUE will certainly improve crop quality and biochemical constituents of the seed such as protein yield and oil yield.

It should be noted that improved ABST will confer plants with improved vigor also under non-stress conditions, resulting in crops having improved biomass and/or yield e.g., elongated fibers for the cotton industry, higher oil content.

The term “fiber” is usually inclusive of thick-walled conducting cells such as vessels and tracheids and to fibrillar aggregates of many individual fiber cells. Hence, the term “fiber” refers to (a) thick-walled conducting and non-conducting cells of the xylem; (b) fibers of extraxylary origin, including those from phloem, bark, ground tissue, and epidermis; and (c) fibers from stems, leaves, roots, seeds, and flowers or inflorescences (such as those of Sorghum vulgare used in the manufacture of brushes and brooms).

Example of fiber producing plants, include, but are not limited to, agricultural crops such as cotton, silk cotton tree (Kapok, Ceiba pentandra), desert willow, creosote bush, winterfat, balsa, kenaf, roselle, jute, sisal abaca, flax, corn, sugar cane, hemp, ramie, kapok, coir, bamboo, spanish moss and Agave spp. (e.g. sisal).

As used herein the phrase “fiber quality” refers to at least one fiber parameter which is agriculturally desired, or required in the fiber industry (further described hereinbelow). Examples of such parameters, include but are not limited to, fiber length, fiber strength, fiber fitness, fiber weight per unit length, maturity ratio and uniformity (further described hereinbelow.

Cotton fiber (lint) quality is typically measured according to fiber length, strength and fineness. Accordingly, the lint quality is considered higher when the fiber is longer, stronger and finer.

As used herein the phrase “fiber yield” refers to the amount or quantity of fibers produced from the fiber producing plant.

As used herein the term “increasing” refers to at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, increase in yield, seed yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of a plant as compared to a native plant [i.e., a plant not modified with the biomolecules (polynucleotide or polypeptides) of the invention, e.g., a non-transformed plant of the same species which is grown under the same (e.g., identical) growth conditions].

The phrase “expressing within the plant an exogenous polynucleotide” as used herein refers to upregulating the expression level of an exogenous polynucleotide within the plant by introducing the exogenous polynucleotide into a plant cell or plant and expressing by recombinant means, as further described herein below.

As used herein “expressing” refers to expression at the mRNA and optionally polypeptide level.

As used herein, the phrase “exogenous polynucleotide” refers to a heterologous nucleic acid sequence which may not be naturally expressed within the plant or which overexpression in the plant is desired. The exogenous polynucleotide may be introduced into the plant in a stable or transient manner, so as to produce a ribonucleic acid (RNA) molecule and/or a polypeptide molecule. It should be noted that the exogenous polynucleotide may comprise a nucleic acid sequence which is identical or partially homologous to an endogenous nucleic acid sequence of the plant.

The term “endogenous” as used herein refers to any polynucleotide or polypeptide which is present and/or naturally expressed within a plant or a cell thereof.

According to some embodiments of the invention, the exogenous polynucleotide of the invention comprises a nucleic acid sequence encoding a polypeptide having an amino acid sequence at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% homologous to the amino acid sequence selected from the group consisting of SEQ ID NOs: 456-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 and 14462.

Homology (e.g., percent homology, identity+similarity) can be determined using any homology comparison software, including for example, the BlastP or TBLASTN software of the National Center of Biotechnology Information (NCBI) such as by using default parameters, when starting from a polypeptide sequence; or the tBLASTX algorithm (available via the NCBI) such as by using default parameters, which compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database.

According to some embodiments of the invention, the term “homology” or “homologous” refers to identity of two or more nucleic acid sequences; or identity of two or more amino acid sequences.

Homologous sequences include both orthologous and paralogous sequences. The term “paralogous” relates to gene-duplications within the genome of a species leading to paralogous genes. The term “orthologous” relates to homologous genes in different organisms due to ancestral relationship.

One option to identify orthologues in monocot plant species is by performing a reciprocal BLAST® search. This may be done by a first BLAST® involving BLASTing the sequence-of-interest against any sequence database, such as the publicly available NCBI database which may be found at: Hypertext Transfer Protocol://World Wide Web (dot) ncbi (dot) nlm (dot) nih (dot) gov. If orthologues in rice were sought, the sequence-of-interest would be BLASTed against, for example, the 28,469 full-length cDNA clones from Oryza sativa Nipponbare available at NCBI. The BLAST® results may be filtered. The full-length sequences of either the filtered results or the non-filtered results are then BLASTed back (second BLAST®) against the sequences of the organism from which the sequence-of-interest is derived. The results of the first and second BLASTs are then compared. An orthologue is identified when the sequence resulting in the highest score (best hit) in the first BLAST® identifies in the second BLAST® the query sequence (the original sequence-of-interest) as the best hit. Using the same rational a paralogue (homolog to a gene in the same organism) is found. In case of large sequence families, the ClustalW program may be used [Hypertext Transfer Protocol://World Wide Web(dot)ebi(dot)ac(dot)uk/Tools/clustalw2/index(dot)html], followed by a neighbor-joining tree (Hypertext Transfer Protocol://en(dot)wikipedia(dot)org/wiki/Neighbor-joining) which helps visualizing the clustering.

According to some embodiments of the invention, the exogenous polynucleotide of the invention encodes a polypeptide having an amino acid sequence at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOs:456-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 and 14462.

According to some embodiments of the invention, the method of increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of a plant is effected by expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% identical to the amino acid sequence selected from the group consisting of SEQ ID NOs:456-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 and 14462, thereby increasing the yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of the plant.

According to some embodiments of the invention, the exogenous polynucleotide encodes a polypeptide consisting of the amino acid sequence set forth by SEQ ID NO:456-774, 8385-10836, 10838-14461 or 14462.

According to an aspect of some embodiments of the invention, the method of increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of a plant, is effected by expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:456-774, 8385-10836, 10838-14461 and 14462, thereby increasing the yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of the plant.

According to an aspect of some embodiments of the invention, there is provided a method of increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide selected from the group consisting of SEQ ID NOs: 456-774, 8385-10836, 10838-14461 and 14462, thereby increasing the yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of the plant.

According to some embodiments of the invention, the exogenous polynucleotide encodes a polypeptide consisting of the amino acid sequence set forth by SEQ ID NO: 456-774, 8385-10836, 10838-14461 or 14462.

According to some embodiments of the invention the exogenous polynucleotide comprises a nucleic acid sequence which is at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, e.g., 100% identical to the nucleic acid sequence selected from the group consisting of SEQ ID NOs:1-455, 775-6485, 6487-6657, 6660-6664, 6666-6701, 6703-6745, 6748-6818, 6820-6821, 6824-6827, 6829-6881, 6883, and 6885-8384.

According to an aspect of some embodiments of the invention, there is provided a method of increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, e.g., 100% identical to the nucleic acid sequence selected from the group consisting of SEQ ID NOs:1-455, 775-6485, 6487-6657, 6660-6664, 6666-6701, 6703-6745, 6748-6818, 6820-6821, 6824-6827, 6829-6881, 6883, and 6885-8384, thereby increasing the yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency of the plant.

According to some embodiments of the invention, the homology is a global homology, i.e., an homology over the entire amino acid or nucleic acid sequences of the invention and not over portions thereof.

According to some embodiments of the invention, the identity is a global identity, i.e., an identity over the entire amino acid or nucleic acid sequences of the invention and not over portions thereof.

Identity (e.g., percent homology) can be determined using any homology comparison software, including for example, the BlastN software of the National Center of Biotechnology Information (NCBI) such as by using default parameters.

According to some embodiments of the invention the exogenous polynucleotide is at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, e.g., 100% identical to the polynucleotide selected from the group consisting of SEQ ID NOs:1-455, 775-6485, 6487-6657, 6660-6664, 6666-6701, 6703-6745, 6748-6818, 6820-6821, 6824-6827, 6829-6881, 6883, and 6885-8384.

According to some embodiments of the invention the exogenous polynucleotide is set forth by SEQ ID NO:1-455, 775-8383 or 8384.

As used herein the term “polynucleotide” refers to a single or double stranded nucleic acid sequence which is isolated and provided in the form of an RNA sequence, a complementary polynucleotide sequence (cDNA), a genomic polynucleotide sequence and/or a composite polynucleotide sequences (e.g., a combination of the above).

The term “isolated” refers to at least partially separated from the natural environment e.g., from a plant cell.

As used herein the phrase “complementary polynucleotide sequence” refers to a sequence, which results from reverse transcription of messenger RNA using a reverse transcriptase or any other RNA dependent DNA polymerase. Such a sequence can be subsequently amplified in vivo or in vitro using a DNA dependent DNA polymerase.

As used herein the phrase “genomic polynucleotide sequence” refers to a sequence derived (isolated) from a chromosome and thus it represents a contiguous portion of a chromosome.

As used herein the phrase “composite polynucleotide sequence” refers to a sequence, which is at least partially complementary and at least partially genomic. A composite sequence can include some exonal sequences required to encode the polypeptide of the present invention, as well as some intronic sequences interposing therebetween. The intronic sequences can be of any source, including of other genes, and typically will include conserved splicing signal sequences. Such intronic sequences may further include cis acting expression regulatory elements.

According to an aspect of some embodiments of the invention, there is provided a method of increasing fertilizer use efficiency (e.g., nitrogen use efficiency) and/or oil content of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% homologous to the amino acid sequence set forth in SEQ ID NO: 10837, thereby increasing the fertilizer use efficiency (e.g., nitrogen use efficiency) and/or oil content of the plant.

According to an aspect of some embodiments of the invention, the method of increasing fertilizer use efficiency (e.g., nitrogen use efficiency) and/or oil content of a plant is effected by expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding the polypeptide set forth in SEQ ID NO: 10837, thereby increasing the fertilizer use efficiency (e.g., nitrogen use efficiency) and/or oil content of a plant.

According to some embodiments of the invention, the exogenous polynucleotide encodes a polypeptide consisting of the amino acid sequence set forth by SEQ ID NO: 10837.

Nucleic acid sequences encoding the polypeptides of the present invention may be optimized for expression. Examples of such sequence modifications include, but are not limited to, an altered G/C content to more closely approach that typically found in the plant species of interest, and the removal of codons atypically found in the plant species commonly referred to as codon optimization.

The phrase “codon optimization” refers to the selection of appropriate DNA nucleotides for use within a structural gene or fragment thereof that approaches codon usage within the plant of interest. Therefore, an optimized gene or nucleic acid sequence refers to a gene in which the nucleotide sequence of a native or naturally occurring gene has been modified in order to utilize statistically-preferred or statistically-favored codons within the plant. The nucleotide sequence typically is examined at the DNA level and the coding region optimized for expression in the plant species determined using any suitable procedure, for example as described in Sardana et al. (1996, Plant Cell Reports 15:677-681). In this method, the standard deviation of codon usage, a measure of codon usage bias, may be calculated by first finding the squared proportional deviation of usage of each codon of the native gene relative to that of highly expressed plant genes, followed by a calculation of the average squared deviation. The formula used is: 1 SDCU=n=1 N [(Xn−Yn)/Yn]2/N, where Xn refers to the frequency of usage of codon n in highly expressed plant genes, where Yn to the frequency of usage of codon n in the gene of interest and N refers to the total number of codons in the gene of interest. A Table of codon usage from highly expressed genes of dicotyledonous plants is compiled using the data of Murray et al. (1989, Nuc Acids Res. 17:477-498).

One method of optimizing the nucleic acid sequence in accordance with the preferred codon usage for a particular plant cell type is based on the direct use, without performing any extra statistical calculations, of codon optimization Tables such as those provided on-line at the Codon Usage Database through the NIAS (National Institute of Agrobiological Sciences) DNA bank in Japan (Hypertext Transfer Protocol://World Wide Web (dot) kazusa (dot) or (dot) jp/codon/). The Codon Usage Database contains codon usage tables for a number of different species, with each codon usage Table having been statistically determined based on the data present in Genbank.

By using the above Tables to determine the most preferred or most favored codons for each amino acid in a particular species (for example, rice), a naturally-occurring nucleotide sequence encoding a protein of interest can be codon optimized for that particular plant species. This is effected by replacing codons that may have a low statistical incidence in the particular species genome with corresponding codons, in regard to an amino acid, that are statistically more favored. However, one or more less-favored codons may be selected to delete existing restriction sites, to create new ones at potentially useful junctions (5′ and 3′ ends to add signal peptide or termination cassettes, internal sites that might be used to cut and splice segments together to produce a correct full-length sequence), or to eliminate nucleotide sequences that may negatively effect mRNA stability or expression.

The naturally-occurring encoding nucleotide sequence may already, in advance of any modification, contain a number of codons that correspond to a statistically-favored codon in a particular plant species. Therefore, codon optimization of the native nucleotide sequence may comprise determining which codons, within the native nucleotide sequence, are not statistically-favored with regards to a particular plant, and modifying these codons in accordance with a codon usage table of the particular plant to produce a codon optimized derivative. A modified nucleotide sequence may be fully or partially optimized for plant codon usage provided that the protein encoded by the modified nucleotide sequence is produced at a level higher than the protein encoded by the corresponding naturally occurring or native gene. Construction of synthetic genes by altering the codon usage is described in for example PCT Patent Application 93/07278.

According to some embodiments of the invention, the exogenous polynucleotide is a non-coding RNA.

As used herein the phrase ‘non-coding RNA” refers to an RNA molecule which does not encode an amino acid sequence (a polypeptide). Examples of such non-coding RNA molecules include, but are not limited to, an antisense RNA, a pre-miRNA (precursor of a microRNA), or a precursor of a Piwi-interacting RNA (piRNA).

Non-limiting examples of non-coding RNA polynucleotides are provided in SEQ ID NOs: 201, 258, 455, 1269, 1312, 2017, 2174, 2278, 2289, 2564, 2565, 2641, 2642, 2643, 2799, 2827, 2828, 2829, 2830, 2835, 2836, 2837, 2852, 2853, 2873, 2877, 3026, 3181, 3250, 3311, 3466, 3480, 4017, 4243, 4339, 4346, 4347, 4508, 4509, 4540, 4541, 4546, 4547, 4548, 4563, 4564, 4565, 4569, 4570, 4581, 4906, 5530, 5955, 5979, 6033, and 6868.

Thus, the invention encompasses nucleic acid sequences described hereinabove; fragments thereof, sequences hybridizable therewith, sequences homologous thereto, sequences encoding similar polypeptides with different codon usage, altered sequences characterized by mutations, such as deletion, insertion or substitution of one or more nucleotides, either naturally occurring or man induced, either randomly or in a targeted fashion.

The invention provides an isolated polynucleotide comprising a nucleic acid sequence at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, e.g., 100% identical to the polynucleotide selected from the group consisting of SEQ ID NOs:1-455, 775-6485, 6487-6657, 6660-6664, 6666-6701, 6703-6745, 6748-6818, 6820-6821, 6824-6827, 6829-6881, 6883, and 6885-8384.

According to some embodiments of the invention the nucleic acid sequence is capable of increasing yield, growth rate, vigor, biomass, oil content, fiber yield, fiber quality, nitrogen use efficiency, fertilizer use efficiency, abiotic stress tolerance and/or water use efficiency of a plant.

According to some embodiments of the invention the isolated polynucleotide comprising the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-455, 775-8383 and 8384.

According to some embodiments of the invention the isolated polynucleotide is set forth by SEQ ID NO:1-455, 775-8383 or 8384.

The invention provides an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises an amino acid sequence at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% homologous to the amino acid sequence selected from the group consisting of SEQ ID NOs: 456-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 and 14462.

According to some embodiments of the invention the amino acid sequence is capable of increasing yield, growth rate, vigor, biomass, oil content, fiber yield, fiber quality, nitrogen use efficiency, fertilizer use efficiency, abiotic stress tolerance and/or water use efficiency of a plant.

The invention provides an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises the amino acid sequence selected from the group consisting of SEQ ID NOs: 456-774, 8385-10836, 10838-14461 and 14462.

According to an aspect of some embodiments of the invention, there is provided a nucleic acid construct comprising the isolated polynucleotide of the invention, and a promoter for directing transcription of the nucleic acid sequence in a host cell.

The invention provides an isolated polypeptide comprising an amino acid sequence at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or more say 100% homologous to an amino acid sequence selected from the group consisting of SEQ ID NOs: 456-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 and 14462.

According to some embodiments of the invention, the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 456-774, 8385-10836, 10838-14461 and 14462.

According to some embodiments of the invention, the polypeptide is set forth by SEQ ID NO: 456-774, 8385-10836, 10838-14461 or 14462.

The invention also encompasses fragments of the above described polypeptides and polypeptides having mutations, such as deletions, insertions or substitutions of one or more amino acids, either naturally occurring or man induced, either randomly or in a targeted fashion.

The term “plant” as used herein encompasses whole plants, ancestors and progeny of the plants and plant parts, including seeds, shoots, stems, roots (including tubers), and plant cells, tissues and organs. The plant may be in any form including suspension cultures, embryos, meristematic regions, callus tissue, leaves, gametophytes, sporophytes, pollen, and microspores. Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including a fodder or forage legume, ornamental plant, food crop, tree, or shrub selected from the list comprising Acacia spp., Acer spp., Actinidia spp., Aesculus spp., Agathis australis, Albizia amara, Alsophila tricolor, Andropogon spp., Arachis spp, Areca catechu, Astelia fragrans, Astragalus cicer, Baikiaea plurijuga, Betula spp., Brassica spp., Bruguiera gymnorrhiza, Burkea africana, Butea frondosa, Cadaba farinosa, Calliandra spp, Camellia sinensis, Canna indica, Capsicum spp., Cassia spp., Centroema pubescens, Chacoomeles spp., Cinnamomum cassia, Coffea arabica, Colophospermum mopane, Coronillia varia, Cotoneaster serotina, Crataegus spp., Cucumis spp., Cupressus spp., Cyathea dealbata, Cydonia oblonga, Cryptomeria japonica, Cymbopogon spp., Cynthea dealbata, Cydonia oblonga, Dalbergia monetaria, Davallia divaricata, Desmodium spp., Dicksonia squarosa, Dibeteropogon amplectens, Dioclea spp, Dolichos spp., Dorycnium rectum, Echinochloa pyramidalis, Ehraffia spp., Eleusine coracana, Eragrestis spp., Erythrina spp., Eucalypfus spp., Euclea schimperi, Eulalia vi/losa, Pagopyrum spp., Feijoa sellowlana, Fragaria spp., Flemingia spp, Freycinetia banksli, Geranium thunbergii, GinAgo biloba, Glycine javanica, Gliricidia spp, Gossypium hirsutum, Grevillea spp., Guibourtia coleosperma, Hedysarum spp., Hemaffhia altissima, Heteropogon contoffus, Hordeum vulgare, Hyparrhenia rufa, Hypericum erectum, Hypeffhelia dissolute, Indigo incamata, Iris spp., Leptarrhena pyrolifolia, Lespediza spp., Lettuca spp., Leucaena leucocephala, Loudetia simplex, Lotonus bainesli, Lotus spp., Macrotyloma axillare, Malus spp., Manihot esculenta, Medicago saliva, Metasequoia glyptostroboides, Musa sapientum, Nicotianum spp., Onobrychis spp., Ornithopus spp., Oryza spp., Peltophorum africanum, Pennisetum spp., Persea gratissima, Petunia spp., Phaseolus spp., Phoenix canariensis, Phormium cookianum, Photinia spp., Picea glauca, Pinus spp., Pisum sativam, Podocarpus totara, Pogonarthria fleckii, Pogonaffhria squarrosa, Populus spp., Prosopis cineraria, Pseudotsuga menziesii, Pterolobium stellatum, Pyrus communis, Quercus spp., Rhaphiolepsis umbellata, Rhopalostylis sapida, Rhus natalensis, Ribes grossularia, Ribes spp., Robinia pseudoacacia, Rosa spp., Rubus spp., Salix spp., Schyzachyrium sanguineum, Sciadopitys vefficillata, Sequoia sempervirens, Sequoiadendron giganteum, Sorghum bicolor, Spinacia spp., Sporobolus fimbriatus, Stiburus alopecuroides, Stylosanthos humilis, Tadehagi spp, Taxodium distichum, Themeda triandra, Trifolium spp., Triticum spp., Tsuga heterophylla, Vaccinium spp., Vicia spp., Vitis vinifera, Watsonia pyramidata, Zantedeschia aethiopica, Zea mays, amaranth, artichoke, asparagus, broccoli, Brussels sprouts, cabbage, canola, carrot, cauliflower, celery, collard greens, flax, kale, lentil, oilseed rape, okra, onion, potato, rice, soybean, straw, sugar beet, sugar cane, sunflower, tomato, squash tea, maize, wheat, barely, rye, oat, peanut, pea, lentil and alfalfa, cotton, rapeseed, canola, pepper, sunflower, tobacco, eggplant, eucalyptus, a tree, an ornamental plant, a perennial grass and a forage crop. Alternatively algae and other non-Viridiplantae can be used for the methods of the present invention.

According to some embodiments of the invention, the plant used by the method of the invention is a crop plant such as rice, maize, wheat, barley, peanut, potato, sesame, olive tree, palm oil, banana, soybean, sunflower, canola, sugarcane, alfalfa, millet, leguminosae (bean, pea), flax, lupinus, rapeseed, tobacco, poplar and cotton.

According to some embodiments of the invention the plant is a dicotyledonous plant.

According to some embodiments of the invention the plant is a monocotyledonous plant.

According to some embodiments of the invention, there is provided a plant cell exogenously expressing the polynucleotide of some embodiments of the invention, the nucleic acid construct of some embodiments of the invention and/or the polypeptide of some embodiments of the invention.

According to some embodiments of the invention, expressing the exogenous polynucleotide of the invention within the plant is effected by transforming one or more cells of the plant with the exogenous polynucleotide, followed by generating a mature plant from the transformed cells and cultivating the mature plant under conditions suitable for expressing the exogenous polynucleotide within the mature plant.

According to some embodiments of the invention, the transformation is effected by introducing to the plant cell a nucleic acid construct which includes the exogenous polynucleotide of some embodiments of the invention and at least one promoter for directing transcription of the exogenous polynucleotide in a host cell (a plant cell). Further details of suitable transformation approaches are provided hereinbelow.

As mentioned, the nucleic acid construct according to some embodiments of the invention comprises a promoter sequence and the isolated polynucleotide of the invention.

According to some embodiments of the invention, the isolated polynucleotide is operably linked to the promoter sequence.

A coding nucleic acid sequence is “operably linked” to a regulatory sequence (e.g., promoter) if the regulatory sequence is capable of exerting a regulatory effect on the coding sequence linked thereto.

As used herein, the term “promoter” refers to a region of DNA which lies upstream of the transcriptional initiation site of a gene to which RNA polymerase binds to initiate transcription of RNA. The promoter controls where (e.g., which portion of a plant) and/or when (e.g., at which stage or condition in the lifetime of an organism) the gene is expressed.

According to some embodiments of the invention, the promoter is heterologous to the isolated polynucleotide and/or to the host cell.

Any suitable promoter sequence can be used by the nucleic acid construct of the present invention. Preferably the promoter is a constitutive promoter, a tissue-specific, or an abiotic stress-inducible promoter.

According to some embodiments of the invention, the promoter is a plant promoter, which is suitable for expression of the exogenous polynucleotide in a plant cell.

Suitable constitutive promoters include, for example, CaMV 35S promoter [SEQ ID NO:14463 (pQFNC); SEQ ID NO:14464 (PJJ 35S from Brachypodium); SEQ ID NO:14465 (Odell et al., Nature 313:810-812, 1985)], Arabidopsis At6669 promoter (SEQ ID NO:14466; see PCT Publication No. WO04081173A2 or the new At6669 promoter (SEQ ID NO:14467); maize Ubi 1 (maize polyubiquitin-1, SEQ ID NO:14468; Christensen et al., Plant Sol. Biol. 18:675-689, 1992; Taylor et al., Plant Cell Rep 12:491-495, 1993); rice actin 1 (SEQ ID NO:14469, McElroy et al., Plant Cell 2:163-171, 1990); pEMU (Last et al., Theor. Appl. Genet. 81:581-588, 1991); CaMV 19S (Nilsson et al., Physiol. Plant 100:456-462, 1997); GOS2 (SEQ ID NO:14470, de Pater et al, Plant J Nov; 2(6):837-44, 1992); Ubi 1 promoter (SEQ ID NO:14471); RBCS promoter (SEQ ID NO:14472); Rice cyclophilin (Bucholz et al, Plant Mol Biol. 25(5):837-43, 1994); Maize H3 histone (Lepetit et al, Mol. Gen. Genet. 231: 276-285, 1992); Actin 2 (An et al, Plant J. 10(1); 107-121, 1996) and Synthetic Super MAS (Ni et al., The Plant Journal 7: 661-76, 1995). Other constitutive promoters include those in U.S. Pat. Nos. 5,659,026, 5,608,149; 5,608,144; 5,604,121; 5,569,597: 5,466,785; 5,399,680; 5,268,463; and 5,608,142.

Suitable tissue-specific promoters include, but not limited to, leaf-specific promoters [e.g., AT5G06690 (Thioredoxin) (high expression, SEQ ID NO:14473), AT5G61520 (AtSTP3) (low expression, SEQ ID NO:14474) described in Buttner et al 2000 Plant, Cell and Environment 23, 175-184, or the promoters described in Yamamoto et al., Plant J. 12:255-265, 1997; Kwon et al., Plant Physiol. 105:357-67, 1994; Yamamoto et al., Plant Cell Physiol. 35:773-778, 1994; Gotor et al., Plant J. 3:509-18, 1993; Orozco et al., Plant Mol. Biol. 23:1129-1138, 1993; and Matsuoka et al., Proc. Natl. Acad. Sci. USA 90:9586-9590, 1993; as well as Arabidopsis STP3 (AT5G61520) promoter (Buttner et al., Plant, Cell and Environment 23:175-184, 2000)], seed-preferred promoters [e.g., Napin (originated from Brassica napus which is characterized by a seed specific promoter activity; Stuitje A. R. et. al. Plant Biotechnology Journal 1 (4): 301-309; SEQ ID NO:14475 from seed specific genes (Simon, et al., Plant Mol. Biol. 5. 191, 1985; Scofield, et al., J. Biol. Chem. 262: 12202, 1987; Baszczynski, et al., Plant Mol. Biol. 14: 633, 1990), rice PG5a (U.S. Pat. No. 7,700,835), early seed development Arabidopsis BAN (SEQ ID NO:14476, US 2009/0031450 A1), late seed development Arabidopsis ABI3 (SEQ ID NO:14477) (Ng et al., Plant Molecular Biology 54: 25-38, 2004), Brazil Nut albumin (Pearson' et al., Plant Mol. Biol. 18: 235-245, 1992), legumin (Ellis, et al. Plant Mol. Biol. 10: 203-214, 1988), Glutelin (rice) (Takaiwa, et al., Mol. Gen. Genet. 208: 15-22, 1986; Takaiwa, et al., FEBS Letts. 221: 43-47, 1987), Zein (Matzke et al Plant Mol Biol, 143). 323-32 1990), napA (Stalberg, et al, Planta 199: 515-519, 1996), Wheat SPA (Albanietal, Plant Cell, 9: 171-184, 1997), sunflower oleosin (Cummins, et al., Plant Mol. Biol. 19: 873-876, 1992)], endosperm specific promoters [e.g., wheat LMW and HMW, glutenin-1 (Thomas and Flavell, The Plant Cell 2:1171-1180, 1990; Mol Gen Genet 216:81-90, 1989; NAR 17:461-2), wheat a, b and g gliadins (EMBO3:1409-15, 1984), Barley ltrl promoter, barley Bl, C, D hordein (Theor Appl Gen 98:1253-62, 1999; Plant J 4:343-55, 1993; Mol Gen Genet 250:750-60, 1996), Barley DOF (Mena et al, The Plant Journal, 116(1): 53-62, 1998), Biz2 (EP99106056.7), Barley SS2 (Guerin and Carbonero Plant Physiology 114: 155-62, 1997), wheat Tarp60 (Kovalchuk et al., Plant Mol Biol 71:81-98, 2009), barley D-hordein (D-Hor) and B-hordein (B-Hor) (Agnelo Furtado, Robert J. Henry and Alessandro Pellegrineschi (2009)], Synthetic promoter (Vicente-Carbajosa et al., Plant J. 13: 629-640, 1998), rice prolamin NRP33, rice-globulin Glb-1 (Wu et al, Plant Cell Physiology 39(8) 885-889, 1998), rice alpha-globulin REB/OHP-1 (Nakase et al. Plant Mol. Biol. 33: 513-S22, 1997), rice ADP-glucose PP (Trans Res 6:157-68, 1997), maize ESR gene family (Plant J 12:235-46, 1997), sorgum gamma-kafirin (PMB 32:1029-35, 1996)], embryo specific promoters [e.g., rice OSH1 (Sato et al, Proc. Natl. Acad. Sci. USA, 93: 8117-8122), KNOX (Postma-Haarsma of al, Plant Mol. Biol. 39:257-71, 1999), rice oleosin (Wu et at, J. Biochem., 123:386, 1998)], and flower-specific promoters [e.g., AtPRP4, chalene synthase (chsA) (Van der Meer, et al., Plant Mol. Biol. 15, 95-109, 1990), LAT52 (Twell et al Mol. Gen Genet. 217:240-245; 1989), Arabidopsis apetala-3 (Tilly et al., Development. 125:1647-57, 1998), Arabidopsis APETALA 1 (AT1G69120, AP1) (SEQ ID NO:14478) (Hempel et al., Development 124:3845-3853, 1997)], and root promoters [e.g., the ROOTP promoter [SEQ ID NO: 14479]; rice ExpB5 and barley ExpB1 promoters (Won et al. Mol. Cells 30: 369-376, 2010); arabidopsis monoterpene synthase (AT3G25820) promoter (Chen et al., Plant Phys 135:1956-66, 2004); arabidopsis Pho1 promoter (SEQ ID NO:14480, Hamburger et al., Plant Cell. 14: 889-902, 2002), which is also slightly induced Pi stress].

Suitable abiotic stress-inducible promoters include, but not limited to, salt-inducible promoters such as RD29A (Yamaguchi-Shinozalei et al., Mol. Gen. Genet. 236:331-340, 1993); drought-inducible promoters such as maize rab17 gene promoter (Pla et. al., Plant Mol. Biol. 21:259-266, 1993), maize rab28 gene promoter (Busk et. al., Plant J. 11:1285-1295, 1997) and maize Ivr2 gene promoter (Pelleschi et. al., Plant Mol. Biol. 39:373-380, 1999); heat-inducible promoters such as heat tomato hsp80-promoter from tomato (U.S. Pat. No. 5,187,267).

The nucleic acid construct of some embodiments of the invention can further include an appropriate selectable marker and/or an origin of replication. According to some embodiments of the invention, the nucleic acid construct utilized is a shuttle vector, which can propagate both in E. coli (wherein the construct comprises an appropriate selectable marker and origin of replication) and be compatible with propagation in cells. The construct according to the present invention can be, for example, a plasmid, a bacmid, a phagemid, a cosmid, a phage, a virus or an artificial chromosome.

The nucleic acid construct of some embodiments of the invention can be utilized to stably or transiently transform plant cells. In stable transformation, the exogenous polynucleotide is integrated into the plant genome and as such it represents a stable and inherited trait. In transient transformation, the exogenous polynucleotide is expressed by the cell transformed but it is not integrated into the genome and as such it represents a transient trait.

There are various methods of introducing foreign genes into both monocotyledonous and dicotyledonous plants (Potrykus, I., Annu. Rev. Plant. Physiol., Plant. Mol. Biol. (1991) 42:205-225; Shimamoto et al., Nature (1989) 338:274-276).

The principle methods of causing stable integration of exogenous DNA into plant genomic DNA include two main approaches:

(i) Agrobacterium-mediated gene transfer: Klee et al. (1987) Annu. Rev. Plant Physiol. 38:467-486; Klee and Rogers in Cell Culture and Somatic Cell Genetics of Plants, Vol. 6, Molecular Biology of Plant Nuclear Genes, eds. Schell, J., and Vasil, L. K., Academic Publishers, San Diego, Calif. (1989) p. 2-25; Gatenby, in Plant Biotechnology, eds. Kung, S. and Arntzen, C. J., Butterworth Publishers, Boston, Mass. (1989) p. 93-112.

(ii) Direct DNA uptake: Paszkowski et al., in Cell Culture and Somatic Cell Genetics of Plants, Vol. 6, Molecular Biology of Plant Nuclear Genes eds. Schell, J., and Vasil, L. K., Academic Publishers, San Diego, Calif. (1989) p. 52-68; including methods for direct uptake of DNA into protoplasts, Toriyama, K. et al. (1988) Bio/Technology 6:1072-1074. DNA uptake induced by brief electric shock of plant cells: Zhang et al. Plant Cell Rep. (1988) 7:379-384. Fromm et al. Nature (1986) 319:791-793. DNA injection into plant cells or tissues by particle bombardment, Klein et al. Bio/Technology (1988) 6:559-563; McCabe et al. Bio/Technology (1988) 6:923-926; Sanford, Physiol. Plant. (1990) 79:206-209; by the use of micropipette systems: Neuhaus et al., Theor. Appl. Genet. (1987) 75:30-36; Neuhaus and Spangenberg, Physiol. Plant. (1990) 79:213-217; glass fibers or silicon carbide whisker transformation of cell cultures, embryos or callus tissue, U.S. Pat. No. 5,464,765 or by the direct incubation of DNA with germinating pollen, DeWet et al. in Experimental Manipulation of Ovule Tissue, eds. Chapman, G. P. and Mantell, S. H. and Daniels, W. Longman, London, (1985) p. 197-209; and Ohta, Proc. Natl. Acad. Sci. USA (1986) 83:715-719.

The Agrobacterium system includes the use of plasmid vectors that contain defined DNA segments that integrate into the plant genomic DNA. Methods of inoculation of the plant tissue vary depending upon the plant species and the Agrobacterium delivery system. A widely used approach is the leaf disc procedure which can be performed with any tissue explant that provides a good source for initiation of whole plant differentiation. See, e.g., Horsch et al. in Plant Molecular Biology Manual A5, Kluwer Academic Publishers, Dordrecht (1988) p. 1-9. A supplementary approach employs the Agrobacterium delivery system in combination with vacuum infiltration. The Agrobacterium system is especially viable in the creation of transgenic dicotyledonous plants.

There are various methods of direct DNA transfer into plant cells. In electroporation, the protoplasts are briefly exposed to a strong electric field. In microinjection, the DNA is mechanically injected directly into the cells using very small micropipettes. In microparticle bombardment, the DNA is adsorbed on microprojectiles such as magnesium sulfate crystals or tungsten particles, and the microprojectiles are physically accelerated into cells or plant tissues.

Following stable transformation plant propagation is exercised. The most common method of plant propagation is by seed. Regeneration by seed propagation, however, has the deficiency that due to heterozygosity there is a lack of uniformity in the crop, since seeds are produced by plants according to the genetic variances governed by Mendelian rules. Basically, each seed is genetically different and each will grow with its own specific traits. Therefore, it is preferred that the transformed plant be produced such that the regenerated plant has the identical traits and characteristics of the parent transgenic plant. Therefore, it is preferred that the transformed plant be regenerated by micropropagation which provides a rapid, consistent reproduction of the transformed plants.

Micropropagation is a process of growing new generation plants from a single piece of tissue that has been excised from a selected parent plant or cultivar. This process permits the mass reproduction of plants having the preferred tissue expressing the fusion protein. The new generation plants which are produced are genetically identical to, and have all of the characteristics of, the original plant. Micropropagation allows mass production of quality plant material in a short period of time and offers a rapid multiplication of selected cultivars in the preservation of the characteristics of the original transgenic or transformed plant. The advantages of cloning plants are the speed of plant multiplication and the quality and uniformity of plants produced.

Micropropagation is a multi-stage procedure that requires alteration of culture medium or growth conditions between stages. Thus, the micropropagation process involves four basic stages: Stage one, initial tissue culturing; stage two, tissue culture multiplication; stage three, differentiation and plant formation; and stage four, greenhouse culturing and hardening. During stage one, initial tissue culturing, the tissue culture is established and certified contaminant-free. During stage two, the initial tissue culture is multiplied until a sufficient number of tissue samples are produced to meet production goals. During stage three, the tissue samples grown in stage two are divided and grown into individual plantlets. At stage four, the transformed plantlets are transferred to a greenhouse for hardening where the plants' tolerance to light is gradually increased so that it can be grown in the natural environment.

According to some embodiments of the invention, the transgenic plants are generated by transient transformation of leaf cells, meristematic cells or the whole plant.

Transient transformation can be effected by any of the direct DNA transfer methods described above or by viral infection using modified plant viruses.

Viruses that have been shown to be useful for the transformation of plant hosts include CaMV, Tobacco mosaic virus (TMV), brome mosaic virus (BMV) and Bean Common Mosaic Virus (BV or BCMV). Transformation of plants using plant viruses is described in U.S. Pat. No. 4,855,237 (bean golden mosaic virus; BGV), EP-A 67,553 (TMV), Japanese Published Application No. 63-14693 (TMV), EPA 194,809 (BV), EPA 278,667 (BV); and Gluzman, Y. et al., Communications in Molecular Biology: Viral Vectors, Cold Spring Harbor Laboratory, New York, pp. 172-189 (1988). Pseudovirus particles for use in expressing foreign DNA in many hosts, including plants are described in WO 87/06261.

According to some embodiments of the invention, the virus used for transient transformations is avirulent and thus is incapable of causing severe symptoms such as reduced growth rate, mosaic, ring spots, leaf roll, yellowing, streaking, pox formation, tumor formation and pitting. A suitable avirulent virus may be a naturally occurring avirulent virus or an artificially attenuated virus. Virus attenuation may be effected by using methods well known in the art including, but not limited to, sub-lethal heating, chemical treatment or by directed mutagenesis techniques such as described, for example, by Kurihara and Watanabe (Molecular Plant Pathology 4:259-269, 2003), Gal-on et al. (1992), Atreya et al. (1992) and Huet et al. (1994).

Suitable virus strains can be obtained from available sources such as, for example, the American Type culture Collection (ATCC) or by isolation from infected plants. Isolation of viruses from infected plant tissues can be effected by techniques well known in the art such as described, for example by Foster and Tatlor, Eds. “Plant Virology Protocols: From Virus Isolation to Transgenic Resistance (Methods in Molecular Biology (Humana Pr), Vol 81)”, Humana Press, 1998. Briefly, tissues of an infected plant believed to contain a high concentration of a suitable virus, preferably young leaves and flower petals, are ground in a buffer solution (e.g., phosphate buffer solution) to produce a virus infected sap which can be used in subsequent inoculations.

Construction of plant RNA viruses for the introduction and expression of non-viral exogenous polynucleotide sequences in plants is demonstrated by the above references as well as by Dawson, W. O. et al., Virology (1989) 172:285-292; Takamatsu et al. EMBO J. (1987) 6:307-311; French et al. Science (1986) 231:1294-1297; Takamatsu et al. FEBS Letters (1990) 269:73-76; and U.S. Pat. No. 5,316,931.

When the virus is a DNA virus, suitable modifications can be made to the virus itself. Alternatively, the virus can first be cloned into a bacterial plasmid for ease of constructing the desired viral vector with the foreign DNA. The virus can then be excised from the plasmid. If the virus is a DNA virus, a bacterial origin of replication can be attached to the viral DNA, which is then replicated by the bacteria. Transcription and translation of this DNA will produce the coat protein which will encapsidate the viral DNA. If the virus is an RNA virus, the virus is generally cloned as a cDNA and inserted into a plasmid. The plasmid is then used to make all of the constructions. The RNA virus is then produced by transcribing the viral sequence of the plasmid and translation of the viral genes to produce the coat protein(s) which encapsidate the viral RNA.

In one embodiment, a plant viral polynucleotide is provided in which the native coat protein coding sequence has been deleted from a viral polynucleotide, a non-native plant viral coat protein coding sequence and a non-native promoter, preferably the subgenomic promoter of the non-native coat protein coding sequence, capable of expression in the plant host, packaging of the recombinant plant viral polynucleotide, and ensuring a systemic infection of the host by the recombinant plant viral polynucleotide, has been inserted. Alternatively, the coat protein gene may be inactivated by insertion of the non-native polynucleotide sequence within it, such that a protein is produced. The recombinant plant viral polynucleotide may contain one or more additional non-native subgenomic promoters. Each non-native subgenomic promoter is capable of transcribing or expressing adjacent genes or polynucleotide sequences in the plant host and incapable of recombination with each other and with native subgenomic promoters. Non-native (foreign) polynucleotide sequences may be inserted adjacent the native plant viral subgenomic promoter or the native and a non-native plant viral subgenomic promoters if more than one polynucleotide sequence is included. The non-native polynucleotide sequences are transcribed or expressed in the host plant under control of the subgenomic promoter to produce the desired products.

In a second embodiment, a recombinant plant viral polynucleotide is provided as in the first embodiment except that the native coat protein coding sequence is placed adjacent one of the non-native coat protein subgenomic promoters instead of a non-native coat protein coding sequence.

In a third embodiment, a recombinant plant viral polynucleotide is provided in which the native coat protein gene is adjacent its subgenomic promoter and one or more non-native subgenomic promoters have been inserted into the viral polynucleotide. The inserted non-native subgenomic promoters are capable of transcribing or expressing adjacent genes in a plant host and are incapable of recombination with each other and with native subgenomic promoters. Non-native polynucleotide sequences may be inserted adjacent the non-native subgenomic plant viral promoters such that the sequences are transcribed or expressed in the host plant under control of the subgenomic promoters to produce the desired product.

In a fourth embodiment, a recombinant plant viral polynucleotide is provided as in the third embodiment except that the native coat protein coding sequence is replaced by a non-native coat protein coding sequence.

The viral vectors are encapsidated by the coat proteins encoded by the recombinant plant viral polynucleotide to produce a recombinant plant virus. The recombinant plant viral polynucleotide or recombinant plant virus is used to infect appropriate host plants. The recombinant plant viral polynucleotide is capable of replication in the host, systemic spread in the host, and transcription or expression of foreign gene(s) (exogenous polynucleotide) in the host to produce the desired protein.

Techniques for inoculation of viruses to plants may be found in Foster and Taylor, eds. “Plant Virology Protocols: From Virus Isolation to Transgenic Resistance (Methods in Molecular Biology (Humana Pr), Vol 81)”, Humana Press, 1998; Maramorosh and Koprowski, eds. “Methods in Virology” 7 vols, Academic Press, New York 1967-1984; Hill, S. A. “Methods in Plant Virology”, Blackwell, Oxford, 1984; Walkey, D. G. A. “Applied Plant Virology”, Wiley, New York, 1985; and Kado and Agrawa, eds. “Principles and Techniques in Plant Virology”, Van Nostrand-Reinhold, New York.

In addition to the above, the polynucleotide of the present invention can also be introduced into a chloroplast genome thereby enabling chloroplast expression.

A technique for introducing exogenous polynucleotide sequences to the genome of the chloroplasts is known. This technique involves the following procedures. First, plant cells are chemically treated so as to reduce the number of chloroplasts per cell to about one. Then, the exogenous polynucleotide is introduced via particle bombardment into the cells with the aim of introducing at least one exogenous polynucleotide molecule into the chloroplasts. The exogenous polynucleotides selected such that it is integratable into the chloroplast's genome via homologous recombination which is readily effected by enzymes inherent to the chloroplast. To this end, the exogenous polynucleotide includes, in addition to a gene of interest, at least one polynucleotide stretch which is derived from the chloroplast's genome. In addition, the exogenous polynucleotide includes a selectable marker, which serves by sequential selection procedures to ascertain that all or substantially all of the copies of the chloroplast genomes following such selection will include the exogenous polynucleotide. Further details relating to this technique are found in U.S. Pat. Nos. 4,945,050; and 5,693,507 which are incorporated herein by reference. A polypeptide can thus be produced by the protein expression system of the chloroplast and become integrated into the chloroplast's inner membrane.

Since processes which increase yield, seed yield, fiber yield, fiber quality, fiber length, growth rate, biomass, vigor, oil content, fertilizer use efficiency, nitrogen use efficiency and/or abiotic stress tolerance of a plant can involve multiple genes acting additively or in synergy (see, for example, in Quesda et al., Plant Physiol. 130:951-063, 2002), the present invention also envisages expressing a plurality of exogenous polynucleotides in a single host plant to thereby achieve superior effect on yield, seed yield, fiber yield, fiber quality, fiber length, growth rate, biomass, vigor, oil content, fertilizer use efficiency, nitrogen use efficiency and/or abiotic stress tolerance of a plant.

Expressing a plurality of exogenous polynucleotides in a single host plant can be effected by co-introducing multiple nucleic acid constructs, each including a different exogenous polynucleotide, into a single plant cell. The transformed cell can than be regenerated into a mature plant using the methods described hereinabove.

Alternatively, expressing a plurality of exogenous polynucleotides in a single host plant can be effected by co-introducing into a single plant-cell a single nucleic-acid construct including a plurality of different exogenous polynucleotides. Such a construct can be designed with a single promoter sequence which can transcribe a polycistronic messenger RNA including all the different exogenous polynucleotide sequences. To enable co-translation of the different polypeptides encoded by the polycistronic messenger RNA, the polynucleotide sequences can be inter-linked via an internal ribosome entry site (IRES) sequence which facilitates translation of polynucleotide sequences positioned downstream of the IRES sequence. In this case, a transcribed polycistronic RNA molecule encoding the different polypeptides described above will be translated from both the capped 5′ end and the two internal IRES sequences of the polycistronic RNA molecule to thereby produce in the cell all different polypeptides. Alternatively, the construct can include several promoter sequences each linked to a different exogenous polynucleotide sequence.

The plant cell transformed with the construct including a plurality of different exogenous polynucleotides, can be regenerated into a mature plant, using the methods described hereinabove.

Alternatively, expressing a plurality of exogenous polynucleotides in a single host plant can be effected by introducing different nucleic acid constructs, including different exogenous polynucleotides, into a plurality of plants. The regenerated transformed plants can then be cross-bred and resultant progeny selected for superior abiotic stress tolerance, water use efficiency, fertilizer use efficiency, growth, biomass, yield and/or vigor traits, using conventional plant breeding techniques.

According to some embodiments of the invention, the method further comprising growing the plant expressing the exogenous polynucleotide under the abiotic stress.

Non-limiting examples of abiotic stress conditions include, salinity, drought, water deprivation, excess of water (e.g., flood, waterlogging), etiolation, low temperature, high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency, nutrient excess, atmospheric pollution and UV irradiation.

According to some embodiments of the invention, the method further comprising growing the plant expressing the exogenous polynucleotide under fertilizer limiting conditions (e.g., nitrogen-limiting conditions). Non-limiting examples include growing the plant on soils with low nitrogen content (40-50% Nitrogen of the content present under normal or optimal conditions), or even under sever nitrogen deficiency (0-10% Nitrogen of the content present under normal or optimal conditions).

Thus, the invention encompasses plants exogenously expressing the polynucleotide(s), the nucleic acid constructs and/or polypeptide(s) of the invention.

Once expressed within the plant cell or the entire plant, the level of the polypeptide encoded by the exogenous polynucleotide can be determined by methods well known in the art such as, activity assays, Western blots using antibodies capable of specifically binding the polypeptide, Enzyme-Linked Immuno Sorbent Assay (ELISA), radio-immuno-assays (RIA), immunohistochemistry, immunocytochemistry, immunofluorescence and the like.

Methods of determining the level in the plant of the RNA transcribed from the exogenous polynucleotide are well known in the art and include, for example, Northern blot analysis, reverse transcription polymerase chain reaction (RT-PCR) analysis (including quantitative, semi-quantitative or real-time RT-PCR) and RNA-in situ hybridization.

The sequence information and annotations uncovered by the present teachings can be harnessed in favor of classical breeding. Thus, sub-sequence data of those polynucleotides described above, can be used as markers for marker assisted selection (MAS), in which a marker is used for indirect selection of a genetic determinant or determinants of a trait of interest (e.g., biomass, growth rate, oil content, yield, abiotic stress tolerance, water use efficiency, nitrogen use efficiency and/or fertilizer use efficiency). Nucleic acid data of the present teachings (DNA or RNA sequence) may contain or be linked to polymorphic sites or genetic markers on the genome such as restriction fragment length polymorphism (RFLP), microsatellites and single nucleotide polymorphism (SNP), DNA fingerprinting (DFP), amplified fragment length polymorphism (AFLP), expression level polymorphism, polymorphism of the encoded polypeptide and any other polymorphism at the DNA or RNA sequence.

Examples of marker assisted selections include, but are not limited to, selection for a morphological trait (e.g., a gene that affects form, coloration, male sterility or resistance such as the presence or absence of awn, leaf sheath coloration, height, grain color, aroma of rice); selection for a biochemical trait (e.g., a gene that encodes a protein that can be extracted and observed; for example, isozymes and storage proteins); selection for a biological trait (e.g., pathogen races or insect biotypes based on host pathogen or host parasite interaction can be used as a marker since the genetic constitution of an organism can affect its susceptibility to pathogens or parasites).

The polynucleotides and polypeptides described hereinabove can be used in a wide range of economical plants, in a safe and cost effective manner.

Plant lines exogenously expressing the polynucleotide or the polypeptide of the invention are screened to identify those that show the greatest increase of the desired plant trait.

The effect of the transgene (the exogenous polynucleotide encoding the polypeptide) on abiotic stress tolerance can be determined using known methods such as detailed below and in the Examples section which follows.

Abiotic stress tolerance—Transformed (i.e., expressing the transgene) and non-transformed (wild type) plants are exposed to an abiotic stress condition, such as water deprivation, suboptimal temperature (low temperature, high temperature), nutrient deficiency, nutrient excess, a salt stress condition, osmotic stress, heavy metal toxicity, anaerobiosis, atmospheric pollution and UV irradiation.

Salinity tolerance assay—Transgenic plants with tolerance to high salt concentrations are expected to exhibit better germination, seedling vigor or growth in high salt. Salt stress can be effected in many ways such as, for example, by irrigating the plants with a hyperosmotic solution, by cultivating the plants hydroponically in a hyperosmotic growth solution (e.g., Hoagland solution), or by culturing the plants in a hyperosmotic growth medium [e.g., 50% Murashige-Skoog medium (MS medium)]. Since different plants vary considerably in their tolerance to salinity, the salt concentration in the irrigation water, growth solution, or growth medium can be adjusted according to the specific characteristics of the specific plant cultivar or variety, so as to inflict a mild or moderate effect on the physiology and/or morphology of the plants (for guidelines as to appropriate concentration see, Bernstein and Kafkafi, Root Growth Under Salinity Stress In: Plant Roots, The Hidden Half 3rd ed. Waisel Y, Eshel A and Kafkafi U. (editors) Marcel Dekker Inc., New York, 2002, and reference therein).

For example, a salinity tolerance test can be performed by irrigating plants at different developmental stages with increasing concentrations of sodium chloride (for example 50 mM, 100 mM, 200 mM, 400 mM NaCl) applied from the bottom and from above to ensure even dispersal of salt. Following exposure to the stress condition the plants are frequently monitored until substantial physiological and/or morphological effects appear in wild type plants. Thus, the external phenotypic appearance, degree of wilting and overall success to reach maturity and yield progeny are compared between control and transgenic plants.

Quantitative parameters of tolerance measured include, but are not limited to, the average wet and dry weight, growth rate, leaf size, leaf coverage (overall leaf area), the weight of the seeds yielded, the average seed size and the number of seeds produced per plant. Transformed plants not exhibiting substantial physiological and/or morphological effects, or exhibiting higher biomass than wild-type plants, are identified as abiotic stress tolerant plants.

Osmotic tolerance test—Osmotic stress assays (including sodium chloride and mannitol assays) are conducted to determine if an osmotic stress phenotype was sodium chloride-specific or if it was a general osmotic stress related phenotype. Plants which are tolerant to osmotic stress may have more tolerance to drought and/or freezing. For salt and osmotic stress germination experiments, the medium is supplemented for example with 50 mM, 100 mM, 200 mM NaCl or 100 mM, 200 mM NaCl, 400 mM mannitol.

Drought tolerance assay/Osmoticum assay—Tolerance to drought is performed to identify the genes conferring better plant survival after acute water deprivation. To analyze whether the transgenic plants are more tolerant to drought, an osmotic stress produced by the non-ionic osmolyte sorbitol in the medium can be performed. Control and transgenic plants are germinated and grown in plant-agar plates for 4 days, after which they are transferred to plates containing 500 mM sorbitol. The treatment causes growth retardation, then both control and transgenic plants are compared, by measuring plant weight (wet and dry), yield, and by growth rates measured as time to flowering.

Conversely, soil-based drought screens are performed with plants overexpressing the polynucleotides detailed above. Seeds from control Arabidopsis plants, or other transgenic plants overexpressing the polypeptide of the invention are germinated and transferred to pots. Drought stress is obtained after irrigation is ceased accompanied by placing the pots on absorbent paper to enhance the soil-drying rate. Transgenic and control plants are compared to each other when the majority of the control plants develop severe wilting. Plants are re-watered after obtaining a significant fraction of the control plants displaying a severe wilting. Plants are ranked comparing to controls for each of two criteria: tolerance to the drought conditions and recovery (survival) following re-watering.

Cold stress tolerance—To analyze cold stress, mature (25 day old) plants are transferred to 4° C. chambers for 1 or 2 weeks, with constitutive light. Later on plants are moved back to greenhouse. Two weeks later damages from chilling period, resulting in growth retardation and other phenotypes, are compared between both control and transgenic plants, by measuring plant weight (wet and dry), and by comparing growth rates measured as time to flowering, plant size, yield, and the like.

Heat stress tolerance—Heat stress tolerance is achieved by exposing the plants to temperatures above 34° C. for a certain period. Plant tolerance is examined after transferring the plants back to 22° C. for recovery and evaluation after 5 days relative to internal controls (non-transgenic plants) or plants not exposed to neither cold or heat stress.

Water use efficiency—can be determined as the biomass produced per unit transpiration. To analyze WUE, leaf relative water content can be measured in control and transgenic plants. Fresh weight (FW) is immediately recorded; then leaves are soaked for 8 hours in distilled water at room temperature in the dark, and the turgid weight (TW) is recorded. Total dry weight (DW) is recorded after drying the leaves at 60° C. to a constant weight. Relative water content (RWC) is calculated according to the following Formula I:

RWC=[(FW−DW)/(TW−DW)]×100  Formula I

Fertilizer use efficiency—To analyze whether the transgenic plants are more responsive to fertilizers, plants are grown in agar plates or pots with a limited amount of fertilizer, as described, for example, Yanagisawa et al (Proc Natl Acad Sci USA. 2004; 101:7833-8). The plants are analyzed for their overall size, time to flowering, yield, protein content of shoot and/or grain. The parameters checked are the overall size of the mature plant, its wet and dry weight, the weight of the seeds yielded, the average seed size and the number of seeds produced per plant. Other parameters that may be tested are: the chlorophyll content of leaves (as nitrogen plant status and the degree of leaf verdure is highly correlated), amino acid and the total protein content of the seeds or other plant parts such as leaves or shoots, oil content, etc. Similarly, instead of providing nitrogen at limiting amounts, phosphate or potassium can be added at increasing concentrations. Again, the same parameters measured are the same as listed above. In this way, nitrogen use efficiency (NUE), phosphate use efficiency (PUE) and potassium use efficiency (KUE) are assessed, checking the ability of the transgenic plants to thrive under nutrient restraining conditions.

Nitrogen use efficiency—To analyze whether the transgenic plants (e.g., Arabidopsis plants) are more responsive to nitrogen, plant are grown in 0.75-3 mM (nitrogen deficient conditions) or 6-10 mM (optimal nitrogen concentration). Plants are allowed to grow for additional 25 days or until seed production. The plants are then analyzed for their overall size, time to flowering, yield, protein content of shoot and/or grain/seed production. The parameters checked can be the overall size of the plant, wet and dry weight, the weight of the seeds yielded, the average seed size and the number of seeds produced per plant. Other parameters that may be tested are: the chlorophyll content of leaves (as nitrogen plant status and the degree of leaf greenness is highly correlated), amino acid and the total protein content of the seeds or other plant parts such as leaves or shoots and oil content. Transformed plants not exhibiting substantial physiological and/or morphological effects, or exhibiting higher measured parameters levels than wild-type plants, are identified as nitrogen use efficient plants.

Nitrogen Use efficiency assay using plantlets—The assay is done according to Yanagisawa-S. et al. with minor modifications (“Metabolic engineering with Dofl transcription factor in plants: Improved nitrogen assimilation and growth under low-nitrogen conditions” Proc. Nall. Acad. Sci. USA 101, 7833-7838). Briefly, transgenic plants which are grown for 7-10 days in 0.5×MS [Murashige-Skoog] supplemented with a selection agent are transferred to two nitrogen-limiting conditions: MS media in which the combined nitrogen concentration (NH4NO₃ and KNO₃) was 0.75 mM (nitrogen deficient conditions) or 6-15 mM (optimal nitrogen concentration). Plants are allowed to grow for additional 30-40 days and then photographed, individually removed from the Agar (the shoot without the roots) and immediately weighed (fresh weight) for later statistical analysis. Constructs for which only T1 seeds are available are sown on selective media and at least 20 seedlings (each one representing an independent transformation event) are carefully transferred to the nitrogen-limiting media. For constructs for which T2 seeds are available, different transformation events are analyzed. Usually, 20 randomly selected plants from each event are transferred to the nitrogen-limiting media allowed to grow for 3-4 additional weeks and individually weighed at the end of that period. Transgenic plants are compared to control plants grown in parallel under the same conditions. Mock-transgenic plants expressing the uidA reporter gene (GUS) under the same promoter or transgenic plants carrying the same promoter but lacking a reporter gene are used as control.

Nitrogen determination—The procedure for N (nitrogen) concentration determination in the structural parts of the plants involves the potassium persulfate digestion method to convert organic N to NO₃ ⁻ (Purcell and King 1996 Argon. J. 88:111-113, the modified Cd⁻ mediated reduction of NO₃ ⁻ to NO₂ (Vodovotz 1996 Biotechniques 20:390-394) and the measurement of nitrite by the Griess assay (Vodovotz 1996, supra). The absorbance values are measured at 550 nm against a standard curve of NaNO₂. The procedure is described in details in Samonte et al. 2006 Agron. J. 98:168-176.

Germination tests—Germination tests compare the percentage of seeds from transgenic plants that could complete the germination process to the percentage of seeds from control plants that are treated in the same manner. Normal conditions are considered for example, incubations at 22° C. under 22-hour light 2-hour dark daily cycles. Evaluation of germination and seedling vigor is conducted between 4 and 14 days after planting. The basal media is 50% MS medium (Murashige and Skoog, 1962 Plant Physiology 15, 473-497).

Germination is checked also at unfavorable conditions such as cold (incubating at temperatures lower than 10° C. instead of 22° C.) or using seed inhibition solutions that contain high concentrations of an osmolyte such as sorbitol (at concentrations of 50 mM, 100 mM, 200 mM, 300 mM, 500 mM, and up to 1000 mM) or applying increasing concentrations of salt (of 50 mM, 100 mM, 200 mM, 300 mM, 500 mM NaCl).

The effect of the transgene on plant's vigor, growth rate, biomass, yield and/or oil content can be determined using known methods.

Plant vigor—The plant vigor can be calculated by the increase in growth parameters such as leaf area, fiber length, rosette diameter, plant fresh weight and the like per time.

Growth rate—The growth rate can be measured using digital analysis of growing plants. For example, images of plants growing in greenhouse on plot basis can be captured every 3 days and the rosette area can be calculated by digital analysis. Rosette area growth is calculated using the difference of rosette area between days of sampling divided by the difference in days between samples.

Evaluation of growth rate can be done by measuring plant biomass produced, rosette area, leaf size or root length per time (can be measured in cm² per day of leaf area).

Relative growth area can be calculated using Formula II.

Relative growth rate area=Regression coefficient of area along time course  Formula II:

Thus, the relative growth area rate is in units of 1/day and length growth rate is in units of 1/day.

Seed yield—Evaluation of the seed yield per plant can be done by measuring the amount (weight or size) or quantity (i.e., number) of dry seeds produced and harvested from 8-16 plants and divided by the number of plants.

For example, the total seeds from 8-16 plants can be collected, weighted using e.g., an analytical balance and the total weight can be divided by the number of plants. Seed yield per growing area can be calculated in the same manner while taking into account the growing area given to a single plant. Increase seed yield per growing area could be achieved by increasing seed yield per plant, and/or by increasing number of plants capable of growing in a given area.

In addition, seed yield can be determined via the weight of 1000 seeds. The weight of 1000 seeds can be determined as follows: seeds are scattered on a glass tray and a picture is taken. Each sample is weighted and then using the digital analysis, the number of seeds in each sample is calculated.

The 1000 seeds weight can be calculated using formula III:

1000 Seed Weight=number of seed in sample/sample weight×1000  Formula III:

The Harvest Index can be calculated using Formula IV

Harvest Index=Average seed yield per plant/Average dry weight  Formula IV:

Grain protein concentration—Grain protein content (g grain protein m⁻²) is estimated as the product of the mass of grain N (g grain N m⁻²) multiplied by the N/protein conversion ratio of k-5.13 (Mosse 1990, supra). The grain protein concentration is estimated as the ratio of grain protein content per unit mass of the grain (g grain protein kg⁻¹ grain).

Fiber length—Fiber length can be measured using fibrograph. The fibrograph system was used to compute length in terms of “Upper Half Mean” length. The upper half mean (UHM) is the average length of longer half of the fiber distribution. The fibrograph measures length in span lengths at a given percentage point (Hypertext Transfer Protocol://World Wide Web (dot) cottoninc (dot) com/ClassificationofCotton/?Pg=4#Length).

According to some embodiments of the invention, increased yield of corn may be manifested as one or more of the following: increase in the number of plants per growing area, increase in the number of ears per plant, increase in the number of rows per ear, number of kernels per ear row, kernel weight, thousand kernel weight (1000-weight), ear length/diameter, increase oil content per kernel and increase starch content per kernel.

As mentioned, the increase of plant yield can be determined by various parameters. For example, increased yield of rice may be manifested by an increase in one or more of the following: number of plants per growing area, number of panicles per plant, number of spikelets per panicle, number of flowers per panicle, increase in the seed filling rate, increase in thousand kernel weight (1000-weight), increase oil content per seed, increase starch content per seed, among others. An increase in yield may also result in modified architecture, or may occur because of modified architecture.

Similarly, increased yield of soybean may be manifested by an increase in one or more of the following: number of plants per growing area, number of pods per plant, number of seeds per pod, increase in the seed filling rate, increase in thousand seed weight (1000-weight), reduce pod shattering, increase oil content per seed, increase protein content per seed, among others. An increase in yield may also result in modified architecture, or may occur because of modified architecture.

Increased yield of canola may be manifested by an increase in one or more of the following: number of plants per growing area, number of pods per plant, number of seeds per pod, increase in the seed filling rate, increase in thousand seed weight (1000-weight), reduce pod shattering, increase oil content per seed, among others. An increase in yield may also result in modified architecture, or may occur because of modified architecture.

Increased yield of cotton may be manifested by an increase in one or more of the following: number of plants per growing area, number of bolls per plant, number of seeds per boll, increase in the seed filling rate, increase in thousand seed weight (1000-weight), increase oil content per seed, improve fiber length, fiber strength, among others. An increase in yield may also result in modified architecture, or may occur because of modified architecture.

Oil content—The oil content of a plant can be determined by extraction of the oil from the seed or the vegetative portion of the plant. Briefly, lipids (oil) can be removed from the plant (e.g., seed) by grinding the plant tissue in the presence of specific solvents (e.g., hexane or petroleum ether) and extracting the oil in a continuous extractor. Indirect oil content analysis can be carried out using various known methods such as Nuclear Magnetic Resonance (NMR) Spectroscopy, which measures the resonance energy absorbed by hydrogen atoms in the liquid state of the sample [See for example, Conway T F. and Earle F R., 1963, Journal of the American Oil Chemists' Society; Springer Berlin/Heidelberg, ISSN: 0003-021X (Print) 1558-9331 (Online)]; the Near Infrared (NI) Spectroscopy, which utilizes the absorption of near infrared energy (1100-2500 nm) by the sample; and a method described in WO/2001/023884, which is based on extracting oil a solvent, evaporating the solvent in a gas stream which forms oil particles, and directing a light into the gas stream and oil particles which forms a detectable reflected light.

Thus, the present invention is of high agricultural value for promoting the yield of commercially desired crops (e.g., biomass of vegetative organ such as poplar wood, or reproductive organ such as number of seeds or seed biomass).

Any of the transgenic plants described hereinabove or parts thereof may be processed to produce a feed, meal, protein or oil preparation, such as for ruminant animals.

The transgenic plants described hereinabove, which exhibit an increased oil content can be used to produce plant oil (by extracting the oil from the plant).

The plant oil (including the seed oil and/or the vegetative portion oil) produced according to the method of the invention may be combined with a variety of other ingredients. The specific ingredients included in a product are determined according to the intended use. Exemplary products include animal feed, raw material for chemical modification, biodegradable plastic, blended food product, edible oil, biofuel, cooking oil, lubricant, biodiesel, snack food, cosmetics, and fermentation process raw material. Exemplary products to be incorporated to the plant oil include animal feeds, human food products such as extruded snack foods, breads, as a food binding agent, aquaculture feeds, fermentable mixtures, food supplements, sport drinks, nutritional food bars, multi-vitamin supplements, diet drinks, and cereal foods. According to some embodiments of the invention, the oil comprises a seed oil.

According to some embodiments of the invention, the oil comprises a vegetative portion oil (oil of the vegetative portion of the plant).

According to some embodiments of the invention, the plant cell forms a part of a plant.

As used herein the term “about” refers to ±10%.

The terms “comprises”, “comprising”, “includes”, “including”, “having” and their conjugates mean “including but not limited to”.

The term “consisting of” means “including and limited to”.

The term “consisting essentially of” means that the composition, method or structure may include additional ingredients, steps and/or parts, but only if the additional ingredients, steps and/or parts do not materially alter the basic and novel characteristics of the claimed composition, method or structure.

As used herein, the singular form “a”, “an” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a compound” or “at least one compound” may include a plurality of compounds, including mixtures thereof.

Throughout this application, various embodiments of this invention may be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.

Whenever a numerical range is indicated herein, it is meant to include any cited numeral (fractional or integral) within the indicated range. The phrases “ranging/ranges between” a first indicate number and a second indicate number and “ranging/ranges from” a first indicate number “to” a second indicate number are used herein interchangeably and are meant to include the first and second indicated numbers and all the fractional and integral numerals therebetween.

As used herein the term “method” refers to manners, means, techniques and procedures for accomplishing a given task including, but not limited to, those manners, means, techniques and procedures either known to, or readily developed from known manners, means, techniques and procedures by practitioners of the chemical, pharmacological, biological, biochemical and medical arts.

It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable subcombination or as suitable in any other described embodiment of the invention. Certain features described in the context of various embodiments are not to be considered essential features of those embodiments, unless the embodiment is inoperative without those elements.

Various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below find experimental support in the following examples.

EXAMPLES

Reference is now made to the following examples, which together with the above descriptions illustrate some embodiments of the invention in a non limiting fashion.

Generally, the nomenclature used herein and the laboratory procedures utilized in the present invention include molecular, biochemical, microbiological and recombinant DNA techniques. Such techniques are thoroughly explained in the literature. See, for example, “Molecular Cloning: A laboratory Manual” Sambrook et al., (1989); “Current Protocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., “Current Protocols in Molecular Biology”, John Wiley and Sons, Baltimore, Md. (1989); Perbal, “A Practical Guide to Molecular Cloning”, John Wiley & Sons, New York (1988); Watson et al., “Recombinant DNA”, Scientific American Books, New York; Birren et al. (eds) “Genome Analysis: A Laboratory Manual Series”, Vols. 1-4, Cold Spring Harbor Laboratory Press, New York (1998); methodologies as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis, J. E., ed. (1994); “Current Protocols in Immunology” Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds), “Basic and Clinical Immunology” (8th Edition), Appleton & Lange, Norwalk, Conn. (1994); Mishell and Shiigi (eds), “Selected Methods in Cellular Immunology”, W. H. Freeman and Co., New York (1980); available immunoassays are extensively described in the patent and scientific literature, see, for example, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521; “Oligonucleotide Synthesis” Gait, M. J., ed. (1984); “Nucleic Acid Hybridization” Hames, B. D., and Higgins S. J., eds. (1985); “Transcription and Translation” Hames, B. D., and Higgins S. J., Eds. (1984); “Animal Cell Culture” Freshney, R. I., ed. (1986); “Immobilized Cells and Enzymes” IRL Press, (1986); “A Practical Guide to Molecular Cloning” Perbal, B., (1984) and “Methods in Enzymology” Vol. 1-317, Academic Press; “PCR Protocols: A Guide To Methods And Applications”, Academic Press, San Diego, Calif. (1990); Marshak et al., “Strategies for Protein Purification and Characterization—A Laboratory Course Manual” CSHL Press (1996); all of which are incorporated by reference as if fully set forth herein. Other general references are provided throughout this document. The procedures therein are believed to be well known in the art and are provided for the convenience of the reader. All the information contained therein is incorporated herein by reference.

General Experimental and Bioinformatics Methods

RNA extraction—Tissues growing at various growth conditions (as described below) were sampled and RNA was extracted using TRIzol Reagent from Invitrogen [Hypertext Transfer Protocol://World Wide Web (dot) invitrogen (dot) com/content (dot)cfm?pageid=469]. Approximately 30-50 mg of tissue was taken from samples. The weighed tissues were ground using pestle and mortar in liquid nitrogen and resuspended in 500 μl of TRIzol Reagent. To the homogenized lysate, 100 μl of chloroform was added followed by precipitation using isopropanol and two washes with 75% ethanol. The RNA was eluted in 30 μl of RNase-free water. RNA samples were cleaned up using Qiagen's RNeasy minikit clean-up protocol as per the manufacturer's protocol (QIAGEN Inc, CA USA). For convenience, each micro-array expression information tissue type has received an expression Set ID.

Correlation analysis—was performed for selected genes according to some embodiments of the invention, in which the characterized parameters (measured parameters according to the correlation IDs) were used as “x axis” for correlation with the tissue transcriptom which was used as the “Y axis”. For each gene and measured parameter a correlation coefficient “R” was calculated [using Pearson correlation test Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html] along with a p-value for the significance of the correlation. When the correlation coefficient (R) between the levels of a gene's expression in a certain tissue and a phenotypic performance across ecotypes/variety/hybrid is high in absolute value (between 0.5-1), there is an association between the gene (specifically the expression level of this gene) the phenotypic characteristic (e.g., improved nitrogen use efficiency, abiotic stress tolerance, yield, growth rate and the like). A positive correlation indicates that the expression of the gene in a certain tissue or developmental stage and the correlation vector (phenotype performance) are positively associated (both, expression and phenotypic performance increase or decrease simultaneously) while a negative correlation indicates a negative association (while the one is increasing the other is decreasing and vice versa).

Example 1 Identification of Genes and Predicted Role Using Bioinformatics Tools

The present inventors have identified polynucleotides which can increase plant yield, seed yield, oil yield, oil content, biomass, growth rate, fiber yield and/or quality, abiotic stress tolerance, nitrogen use efficiency and/or vigor of a plant, as follows. The nucleotide sequence datasets used here were from publicly available databases or from sequences obtained using the Solexa technology (e.g. Barley and Sorghum). Sequence data from 100 different plant species was introduced into a single, comprehensive database. Other information on gene expression, protein annotation, enzymes and pathways were also incorporated. Major databases used include:

Genomes

-   Arabidopsis genome [TAIR genome version 8 (Hypertext Transfer     Protocol://World Wide Web (dot) arabidopsis (dot) org/)]; -   Rice genome [build 6.0 (Hypertext Transfer Protocol://rice (dot)     plantbiology(dot)msu(dot)edu/index. shtml]; -   Poplar [Populus trichocarpa release 1.1 from JGI (assembly release     v1.0) (Hypertext Transfer Protocol://World Wide Web (dot) genome     (dot) jgi-psf (dot) org/)]; -   Brachypodium [JGI 4× assembly, Hypertext Transfer Protocol://World     Wide Web (dot) brachpodium (dot) org)]; -   Soybean [DOE-JGI SCP, version Glymal (Hypertext Transfer     Protocol://World Wide Web (dot) phytozome (dot) net/)]; -   Grape [French-Italian Public Consortium for Grapevine Genome     Characterization grapevine genome (Hypertext Transfer Protocol://     World Wide Web (dot) genoscope (dot) cns (dot) fr/)]; -   Castobean [TIGR/J Craig Venter Institute 4× assembly [(Hypertext     Transfer Protocol://msc (dot) jcvi (dot) org/r communis]; -   Sorghum [DOE-JGI SCP, version Sbi1 [Hypertext Transfer     Protocol://World Wide Web (dot) phytozome (dot) net/)]; -   Partially assembled genome of Maize [Hypertext Transfer     Protocol://maizesequence (dot) org/];

Expressed EST and mRNA Sequences were Extracted from the Following Databases:

-   EST and RNA sequences from NCBI (Hypertext Transfer Protocol://World     Wide Web (dot) ncbi (dot) nlm (dot) nih (dot) gov/dbEST/); -   RefSeq (Hypertext Transfer Protocol://World Wide Web (dot) ncbi     (dot) nlm (dot) nih (dot) gov/RefSeq/); -   TAIR (Hypertext Transfer Protocol://World Wide Web (dot) arabidopsis     (dot) org/);

Protein and Pathway Databases

-   Uniprot [Hypertext Transfer Protocol://World Wide Web (dot) uniprot     (dot) org/]. -   AraCyc [Hypertext Transfer Protocol://World Wide Web (dot)     arabidopsis (dot) org/biocyc/index (dot) jsp]. -   ENZYME [Hypertext Transfer Protocol://expasy (dot) org/enzyme/].

Microarray Datasets were Downloaded from:

-   GEO (Hypertext Transfer Protocol://World Wide     Web.ncbi.nlm.nih.gov/geo/) TAIR (Hypertext Transfer Protocol://World     Wide Web.arabidopsis.org/). -   Proprietary microarray data (See WO2008/122980) and Examples 2-9     below.

QTL and SNPs Information

-   Gramene [Hypertext Transfer Protocol://World Wide Web (dot) gramene     (dot) org/qtl/]. -   Panzea [Hypertext Transfer Protocol://World Wide Web (dot) panzea     (dot) org/index (dot) html].

Database Assembly—was performed to build a wide, rich, reliable annotated and easy to analyze database comprised of publicly available genomic mRNA, ESTs DNA sequences, data from various crops as well as gene expression, protein annotation and pathway data QTLs, and other relevant information.

Database assembly is comprised of a toolbox of gene refining, structuring, annotation and analysis tools enabling to construct a tailored database for each gene discovery project. Gene refining and structuring tools enable to reliably detect splice variants and antisense transcripts, generating understanding of various potential phenotypic outcomes of a single gene. The capabilities of the “LEADS” platform of Compugen LTD for analyzing human genome have been confirmed and accepted by the scientific community [see e.g., “Widespread Antisense Transcription”, Yelin, et al. (2003) Nature Biotechnology 21, 379-85; “Splicing of Alu Sequences”, Lev-Maor, et al. (2003) Science 300 (5623), 1288-91; “Computational analysis of alternative splicing using EST tissue information”, Xie H et al. Genomics 2002], and have been proven most efficient in plant genomics as well.

EST clustering and gene assembly—For gene clustering and assembly of organisms with available genome sequence data (arabidopsis, rice, castorbean, grape, brachypodium, poplar, soybean, sorghum) the genomic LEADS version (GANG) was employed. This tool allows most accurate clustering of ESTs and mRNA sequences on genome, and predicts gene structure as well as alternative splicing events and anti-sense transcription.

For organisms with no available full genome sequence data, “expressed LEADS” clustering software was applied.

Gene annotation—Predicted genes and proteins were annotated as follows:

BLAST® search [Hypertext Transfer Protocol://blast(dot)ncbi(dot)nlm(dot) nih(dot)gov/Blast(dot)cgi] against all plant UniProt [Hypertext Transfer Protocol://World Wide Web(dot)uniprot(dot)org/] sequences was performed. Open reading frames of each putative transcript were analyzed and longest ORF with higher number of homologues was selected as predicted protein of the transcript. The predicted proteins were analyzed by InterPro [Hypertext Transfer Protocol://World Wide Web(dot)ebi(dot)ac(dot)uk/interpro/].

BLAST® against proteins from AraCyc and ENZYME databases was used to map the predicted transcripts to AraCyc pathways.

Predicted proteins from different species were compared using BLAST® algorithm [Hypertext Transfer Protocol://World Wide Web(dot)ncbi(dot)nlm(dot)nih (dot)gov/Blast(dot)cgi] to validate the accuracy of the predicted protein sequence, and for efficient detection of orthologs.

Gene expression profiling—Several data sources were exploited for gene expression profiling which combined microarray data and digital expression profile (see below). According to gene expression profile, a correlation analysis was performed to identify genes which are co-regulated under different developmental stages and environmental conditions and which are associated with different phenotypes.

Publicly available microarray datasets were downloaded from TAR and NCBI GEO sites, renormalized, and integrated into the database. Expression profiling is one of the most important resource data for identifying genes important for yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance of plants and nitrogen use efficiency.

A digital expression profile summary was compiled for each cluster according to all keywords included in the sequence records comprising the cluster. Digital expression, also known as electronic Northern Blot, is a tool that displays virtual expression profile based on the EST sequences forming the gene cluster. The tool provides the expression profile of a cluster in terms of plant anatomy (e.g., the tissue/organ in which the gene is expressed), developmental stage (e.g., the developmental stages at which a gene can be found/expressed) and profile of treatment (provides the physiological conditions under which a gene is expressed such as drought, cold, pathogen infection, etc). Given a random distribution of ESTs in the different clusters, the digital expression provides a probability value that describes the probability of a cluster having a total of N ESTs to contain X ESTs from a certain collection of libraries. For the probability calculations, the following is taken into consideration: a) the number of ESTs in the cluster, b) the number of ESTs of the implicated and related libraries, c) the overall number of ESTs available representing the species. Thereby clusters with low probability values are highly enriched with ESTs from the group of libraries of interest indicating a specialized expression.

Recently, the accuracy of this system was demonstrated by Portnoy et al., 2009 (Analysis Of The Melon Fruit Transcriptome Based On 454 Pyrosequencing) in: Plant & Animal Genomes XVII Conference, San Diego, Calif. Transcriptomic analysis, based on relative EST abundance in data was performed by 454 pyrosequencing of cDNA representing mRNA of the melon fruit. Fourteen double strand cDNA samples obtained from two genotypes, two fruit tissues (flesh and rind) and four developmental stages were sequenced. GS FLX pyrosequencing (Roche/454 Life Sciences) of non-normalized and purified cDNA samples yielded 1,150,657 expressed sequence tags that assembled into 67,477 unigenes (32,357 singletons and 35,120 contigs). Analysis of the data obtained against the Cucurbit Genomics Database [Hypertext Transfer Protocol://World Wide Web (dot) icugi (dot) org/] confirmed the accuracy of the sequencing and assembly. Expression patterns of selected genes fitted well their qRT-PCR data.

Example 2 Production of Arabidopsis Transcriptom and High Throughput Correlation Analysis of Yield, Biomass and/or Vigor Related Parameters Using 44K Arabidopsis Full Genome Oligonucleotide Micro-Array

To produce a high throughput correlation analysis, the present inventors utilized an Arabidopsis thaliana oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. The array oligonucleotide represents about 40,000 A. thaliana genes and transcripts designed based on data from the TIGR ATH1 v.5 database and Arabidopsis MPSS (University of Delaware) databases. To define correlations between the levels of RNA expression and yield, biomass components or vigor related parameters, various plant characteristics of 15 different Arabidopsis ecotypes were analyzed. Among them, nine ecotypes encompassing the observed variance were selected for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html].

Experimental Procedures

Analyzed Arabidopsis tissues—Five tissues at different developmental stages including root, leaf, flower at anthesis, seed at 5 days after flowering (DAF) and seed at 12 DAF, representing different plant characteristics, were sampled and RNA was extracted as described as described hereinabove under “GENERAL EXPERIMENTAL AND BIOINFORMATICS METHODS”. For convenience, each micro-array expression information tissue type has received a Set ID as summarized in Table 1 below.

TABLE 1 Tissues used for Arabidopsis transcriptom expression sets Expression Set Set ID Root at reproductive stage 1 Seed 5 DAF at reproductive stage 2 Seed 12 DAF at reproductive stage 3 Flower at reproductive stage 4 Leaf at reproductive stage 5 Table 1: Provided are the identification (ID) digits of each of the Arabidopsis expression sets (1-5). DAF = days after flowering.

Yield components and vigor related parameters assessment—Eight out of the nine Arabidopsis ecotypes were used in each of 5 repetitive blocks (named A, B, C, D and E), each containing 20 plants per plot. The plants were grown in a greenhouse at controlled conditions in 22° C., and the N:P:K fertilizer (20:20:20; weight ratios) [nitrogen (N), phosphorus (P) and potassium (K)] was added. During this time data was collected, documented and analyzed. Additional data was collected through the seedling stage of plants grown in a tissue culture in vertical grown transparent agar plates. Most of chosen parameters were analyzed by digital imaging.

Digital imaging in Tissue culture—A laboratory image acquisition system was used for capturing images of plantlets sawn in square agar plates. The image acquisition system consists of a digital reflex camera (Canon EOS 300D) attached to a 55 mm focal length lens (Canon EF-S series), mounted on a reproduction device (Kaiser RS), which included 4 light units (4×150 Watts light bulb) and located in a darkroom.

Digital imaging in Greenhouse—The image capturing process was repeated every 3-4 days starting at day 7 till day 30. The same camera attached to a 24 mm focal length lens (Canon EF series), placed in a custom made iron mount, was used for capturing images of larger plants sawn in white tubs in an environmental controlled greenhouse. The white tubs were square shape with measurements of 36×26.2 cm and 7.5 cm deep. During the capture process, the tubs were placed beneath the iron mount, while avoiding direct sun light and casting of shadows. This process was repeated every 3-4 days for up to 30 days.

An image analysis system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.37, Java based image processing program, which was developed at the U.S. National Institutes of Health and is freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/. Images were captured in resolution of 6 Mega Pixels (3072×2048 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute).

Leaf analysis—Using the digital analysis leaves data was calculated, including leaf number, area, perimeter, length and width. On day 30, 3-4 representative plants were chosen from each plot of blocks A, B and C. The plants were dissected, each leaf was separated and was introduced between two glass trays, a photo of each plant was taken and the various parameters (such as leaf total area, laminar length etc.) were calculated from the images. The blade circularity was calculated as laminar width divided by laminar length.

Root analysis—During 17 days, the different ecotypes were grown in transparent agar plates. The plates were photographed every 3 days starting at day 7 in the photography room and the roots development was documented (see examples in FIGS. 3A-3F). The growth rate of roots was calculated according to Formula V.

Relative growth rate of root coverage=Regression coefficient of root coverage along time course.  Formula V:

Vegetative growth rate analysis—was calculated according to Formula VI. The analysis was ended with the appearance of overlapping plants.

Relative vegetative growth rate area=Regression coefficient of vegetative area along time course.  Formula VI

For comparison between ecotypes the calculated rate was normalized using plant developmental stage as represented by the number of true leaves. In cases where plants with 8 leaves had been sampled twice (for example at day 10 and day 13), only the largest sample was chosen and added to the Anova comparison.

Seeds in siliques analysis—On day 70, 15-17 siliques were collected from each plot in blocks D and E. The chosen siliques were light brown color but still intact. The siliques were opened in the photography room and the seeds were scatter on a glass tray, a high resolution digital picture was taken for each plot. Using the images the number of seeds per silique was determined.

Seeds average weight—At the end of the experiment all seeds from plots of blocks A-C were collected. An average weight of 0.02 grams was measured from each sample, the seeds were scattered on a glass tray and a picture was taken. Using the digital analysis, the number of seeds in each sample was calculated.

Oil percentage in seeds—At the end of the experiment all seeds from plots of blocks A-C were collected. Columbia seeds from 3 plots were mixed grounded and then mounted onto the extraction chamber. 210 ml of n-Hexane (Cat No. 080951 Biolab Ltd.) were used as the solvent. The extraction was performed for 30 hours at medium heat 50° C. Once the extraction has ended the n-Hexane was evaporated using the evaporator at 35° C. and vacuum conditions. The process was repeated twice. The information gained from the Soxhlet extractor (Soxhlet, F. Die gewichtsanalytische Bestimmung des Milchfettes, Polytechnisches J. (Dingler's) 1879, 232, 461) was used to create a calibration curve for the Low Resonance NMR. The content of oil of all seed samples was determined using the Low Resonance NMR (MARAN Ultra-Oxford Instrument) and its MultiQuant sowftware package.

Silique length analysis—On day 50 from sowing, 30 siliques from different plants in each plot were sampled in block A. The chosen siliques were green-yellow in color and were collected from the bottom parts of a grown plant's stem. A digital photograph was taken to determine silique's length.

Dry weight and seed yield—On day 80 from sowing, the plants from blocks A-C were harvested and left to dry at 30° C. in a drying chamber. The biomass and seed weight of each plot was separated, measured and divided by the number of plants. Dry weight=total weight of the vegetative portion above ground (excluding roots) after drying at 30° C. in a drying chamber; Seed yield per plant=total seed weight per plant (gr).

Oil yield—The oil yield was calculated using Formula VII.

Seed Oil yield=Seed yield per plant (gr.)*Oil % in seed.  Formula VII:

Harvest Index (seed)—The harvest index was calculated using Formula IV (described above): Harvest Index=Average seed yield per plant/Average dry weight.

Experimental Results

Nine different Arabidopsis ecotypes were grown and characterized for 18 parameters (named as vectors).

TABLE 2 Arabidopsis correlated parameters (vectors) Correlated parameter with Correlation ID Seeds per silique (number) 1 Harvest Index (value) 2 seed yield per plant (gr) 3 Dry matter per plant (gr) 4 Total Leaf Area per plant (cm) 5 Oil % per seed (percent) 6 Oil yield per plant (mg) 7 relative root growth (cm/day) 8 root length day 7 (cm) 9 root length day 13 (cm) 10 fresh weight (gr) 11 seed weight (gr) 12 Vegetative growth rate (cm²/day) 13 Lamina length (cm) 14 Lamina width (cm) 15 Leaf width/length (ratio) 16 Blade circularity (cm) 17 Silique length (cm) 18 Table 2: Provided are the Arabidopsis correlated parameters (correlation ID Nos. 1-18). Abbreviations: Cm = centimeter(s); gr = gram(s); mg = milligram(s).

The characterized values are summarized in Table 3 and 4 below and the correlation analysis is provided in Table 5 below.

TABLE 3 Measured parameters in Arabidopsis ecotypes Ecotype/ Correlation ID No. Line-1 Line-2 Line-3 Line-4 Line-5 1 45.44 53.47 58.47 35.27 48.56 2 0.53 0.35 0.56 0.33 0.37 3 0.34 0.44 0.59 0.42 0.61 4 0.64 1.27 1.05 1.28 1.69 5 46.86 109.89 58.36 56.8 114.66 6 34.42 31.19 38.05 27.76 35.49 7 118.63 138.73 224.06 116.26 218.27 8 0.631 0.664 1.176 1.089 0.907 9 0.937 1.759 0.701 0.728 0.991 10 4.419 8.53 5.621 4.834 5.957 11 1.51 3.607 1.935 2.082 3.556 12 0.02031238 0.02302244 0.02522553 0.03444936 0.02021001 13 0.31258158 0.37755231 0.4841254 0.47415969 0.42508143 14 2.76683 3.54357 3.27353 3.78465 3.68982 15 1.38477 1.69708 1.45982 1.37418 1.82816 16 0.352785 0.287757 0.315993 0.258499 0.356279 17 0.508828 0.48083 0.45029 0.369857 0.500566 18 1.06 1.26 1.31 1.47 1.24 Table 3: Provided are the values of each of the parameters measured in Arabidopsis ecotypes (lines 1-5) using the correlation ID numbers described in Table 2 hereinabove.

TABLE 4 Measured parameters in Arabidopsis ecotypes-continue Ecotype/ Correlation ID No. Line-6 Line-7 Line-8 Line-9 1 37 39.38 40.53 25.53 2 0.32 0.45 0.51 0.41 3 0.43 0.36 0.62 0.55 4 1.34 0.81 1.21 1.35 5 110.82 88.49 121.79 93.04 6 32.91 31.56 30.79 34.02 7 142.11 114.15 190.06 187.62 8 0.774 0.606 0.701 0.782 9 1.163 1.284 1.414 1.251 10 6.372 5.649 7.06 7.041 11 4.338 3.467 3.479 3.71 12 0.02634353 0.02048623 0.02260485 0.02352516 13 0.64454891 0.42961167 0.38423782 0.47130278 14 4.59654 3.87735 3.71722 4.14899 15 1.64999 1.51005 1.81691 1.66772 16 0.272645 0.304707 0.335145 0.306598 17 0.375805 0.393745 0.491283 0.408787 18 1.09 1.18 1.18 1 Table 4: Provided are the values of each of the parameters measured in Arabidopsis ecotypes (lines 6-9) using the correlation ID numbers described in Table 2 hereinabove.

TABLE 5 Correlation between the expression level of selected genes of some embodiments of the invention in various tissues and the phenotypic performance under normal conditions across Arabidopsis accessions Gene Exp. Corr. Gene Exp. Corr. Name R P value set ID Name R P value set ID LYD289 0.92 3.17E−03 2 18 LYD289 0.90 2.54E−03 4 18 LYD289 0.75 3.34E−02 5 3 LYD289 0.75 3.25E−02 5 7 LYD290 0.77 2.42E−02 1 18 LYD290 0.79 3.33E−02 2 9 LYD290 0.71 4.87E−02 3 2 LYD291 0.89 7.19E−03 2 2 LYD291 0.76 4.58E−02 2 6 LYD291 0.71 4.76E−02 3 18 LYD292 0.70 5.11E−02 1 1 LYD292 0.73 4.16E−02 4 8 LYD292 0.74 3.48E−02 5 12 LYD292 0.81 1.44E−02 5 18 LYD293 0.71 4.72E−02 3 18 LYD293 0.72 4.28E−02 5 3 LYD293 0.74 3.65E−02 5 7 LYD293 0.76 3.03E−02 5 8 LYD294 0.74 3.55E−02 1 18 LYD294 0.81 1.57E−02 5 12 LYD294 0.79 2.01E−02 5 18 LYD295 0.73 3.83E−02 1 18 LYD295 0.80 3.03E−02 2 2 LYD295 0.79 2.08E−02 3 3 LYD295 0.71 4.92E−02 3 7 LYD295 0.72 4.32E−02 5 1 LYD296 0.76 4.69E−02 2 18 LYD296 0.76 4.57E−02 2 3 LYD296 0.77 4.34E−02 2 7 LYD296 0.86 5.77E−03 3 18 LYD297 0.86 1.23E−02 2 1 LYD297 0.76 4.69E−02 2 18 LYD297 0.84 8.28E−03 3 4 LYD297 0.76 3.03E−02 5 12 LYD297 0.75 3.32E−02 5 18 LYD298 0.70 7.71E−02 2 1 LYD298 0.72 6.93E−02 2 18 LYD298 0.88 3.55E−03 3 12 LYD298 0.75 3.28E−02 3 18 LYD299 0.85 7.67E−03 1 12 LYD299 0.76 2.79E−02 1 18 LYD299 0.71 7.32E−02 2 14 LYD299 0.87 1.19E−02 2 13 LYD299 0.84 9.28E−03 3 12 LYD299 0.98 1.37E−05 4 12 LYD299 0.85 7.82E−03 5 12 LYD300 0.80 1.68E−02 1 12 LYD300 0.75 3.08E−02 1 18 LYD300 0.73 6.21E−02 2 9 LYD300 0.86 6.54E−03 3 12 LYD300 0.78 2.26E−02 3 18 LYD301 0.73 3.94E−02 1 3 LYD301 0.77 2.55E−02 1 7 LYD301 0.84 1.68E−02 2 4 LYD301 0.80 3.03E−02 2 3 LYD301 0.77 4.39E−02 2 7 LYD301 0.71 4.99E−02 3 15 LYD301 0.89 3.27E−03 3 10 LYD301 0.71 5.06E−02 4 4 LYD301 0.72 4.21E−02 4 15 LYD301 0.80 1.82E−02 4 3 LYD301 0.78 2.24E−02 4 7 LYD301 0.76 2.94E−02 4 13 LYD301 0.81 1.59E−02 5 4 LYD301 0.85 6.99E−03 5 15 LYD301 0.73 4.04E−02 5 5 LYD302 0.83 2.04E−02 2 16 LYD302 0.74 5.73E−02 2 17 LYD302 0.91 1.50E−03 3 18 LYD302 0.76 2.85E−02 4 18 LYD303 0.83 1.00E−02 1 15 LYD303 0.76 2.83E−02 1 5 LYD303 0.72 4.40E−02 3 15 LYD303 0.87 5.08E−03 3 10 LYD303 0.80 1.67E−02 4 18 LYD304 0.80 2.92E−02 2 2 LYD304 0.70 5.27E−02 3 3 LYD305 0.93 2.70E−03 2 4 LYD305 0.83 2.01E−02 2 15 LYD305 0.73 6.26E−02 2 3 LYD305 0.76 2.94E−02 3 18 LYD306 0.87 4.65E−03 1 1 LYD306 0.86 6.39E−03 1 18 LYD306 0.74 5.59E−02 2 9 LYD306 0.82 1.34E−02 3 9 LYD306 0.70 5.24E−02 3 10 LYD306 0.72 4.51E−02 4 1 LYD306 0.92 1.36E−03 5 18 LYD307 0.89 2.95E−03 3 3 LYD307 0.79 1.94E−02 3 7 LYD308 0.74 3.52E−02 1 9 LYD308 0.71 7.45E−02 2 2 LYD308 0.70 5.29E−02 5 12 LYD308 0.97 5.57E−05 5 14 LYD308 0.76 2.86E−02 5 11 LYD308 0.86 6.25E−03 5 13 LYD309 0.84 8.79E−03 3 16 LYD309 0.83 1.08E−02 4 1 LYD310 0.85 1.60E−02 2 12 LYD310 0.74 5.68E−02 2 13 LYD310 0.95 3.36E−04 3 16 LYD310 0.73 4.17E−02 3 17 LYD310 0.75 3.39E−02 5 3 LYD310 0.91 1.78E−03 5 6 LYD310 0.87 4.96E−03 5 7 LYD311 0.73 4.06E−02 3 12 LYD311 0.80 1.76E−02 3 18 LYD312 0.72 6.60E−02 2 18 LYD312 0.74 3.70E−02 3 12 LYD312 0.73 3.97E−02 5 18 LYD313 0.75 3.13E−02 4 1 LYD313 0.87 4.72E−03 5 12 LYD315 0.83 2.12E−02 2 2 LYD315 0.73 6.03E−02 2 6 LYD315 0.72 4.45E−02 3 3 LYD315 0.81 1.41E−02 4 18 LYD316 0.76 4.96E−02 2 1 LYD316 0.79 3.36E−02 2 18 LYD316 0.84 9.29E−03 3 3 LYD316 0.87 4.46E−03 3 7 LYD318 0.75 3.33E−02 5 2 LYD319 0.77 4.30E−02 2 4 LYD319 0.84 1.83E−02 2 15 LYD319 0.77 4.11E−02 2 5 LYD319 0.78 2.17E−02 3 1 LYD319 0.75 3.34E−02 3 17 LYD319 0.85 7.55E−03 4 6 LYD319 0.76 2.92E−02 4 7 LYD320 0.74 3.49E−02 3 14 LYD320 0.80 1.69E−02 3 13 LYD321 0.76 2.92E−02 4 1 LYD321 0.71 4.76E−02 5 17 LYD322 0.87 4.62E−03 5 4 LYD322 0.79 2.07E−02 5 15 LYD323 0.70 5.23E−02 1 16 LYD323 0.77 4.25E−02 2 2 LYD323 0.73 4.15E−02 4 1 LYD323 0.87 4.54E−03 4 17 LYD323 0.92 1.17E−03 5 1 LYD323 0.85 8.20E−03 5 17 LYD324 0.89 2.94E−03 3 12 LYD324 0.71 4.65E−02 3 18 LYD324 0.73 4.16E−02 5 4 LYD324 0.82 1.18E−02 5 3 LYD324 0.74 3.52E−02 5 7 LYD325 0.81 1.55E−02 1 12 LYD325 0.75 3.21E−02 3 12 LYD325 0.77 2.52E−02 3 18 LYD326 0.77 2.60E−02 4 9 LYD326 0.73 3.87E−02 4 10 LYD327 0.78 2.35E−02 3 16 LYD327 0.78 2.27E−02 5 18 LYD328 0.72 4.20E−02 3 3 LYD328 0.78 2.32E−02 5 12 LYD328 0.89 2.68E−03 5 8 LYD329 0.71 4.80E−02 1 8 LYD329 0.79 3.41E−02 2 1 LYD329 0.92 3.64E−03 2 17 LYD329 0.78 2.25E−02 3 3 LYD329 0.74 3.57E−02 3 13 LYD329 0.81 1.41E−02 3 8 LYD329 0.90 2.51E−03 5 8 LYD330 0.74 3.63E−02 3 2 LYD331 0.74 3.50E−02 1 6 LYD331 0.74 3.72E−02 1 7 LYD331 0.72 4.38E−02 3 3 LYD331 0.76 2.77E−02 3 7 LYD331 0.73 3.85E−02 3 17 LYD331 0.75 3.29E−02 4 3 LYD331 0.75 3.36E−02 4 6 LYD331 0.81 1.54E−02 4 7 LYD331 0.75 3.15E−02 5 3 LYD331 0.76 3.00E−02 5 6 LYD331 0.82 1.18E−02 5 7 LYD332 0.78 2.17E−02 1 6 LYD332 0.74 3.70E−02 3 16 LYD332 0.81 1.45E−02 3 17 LYD334 0.72 6.61E−02 2 3 LYD334 0.82 2.30E−02 2 6 LYD334 0.80 3.09E−02 2 7 LYD334 0.76 4.96E−02 2 8 LYD334 0.78 2.19E−02 3 12 LYD334 0.73 4.01E−02 4 3 LYD334 0.70 5.27E−02 4 7 LYD335 0.74 5.55E−02 2 2 LYD337 0.77 4.25E−02 2 10 LYD337 0.76 3.03E−02 3 3 LYD338 0.75 3.38E−02 3 2 LYD338 0.74 3.55E−02 4 13 LYD338 0.82 1.31E−02 5 6 LYD338 0.79 1.88E−02 5 7 LYD339 0.79 3.58E−02 2 2 LYD339 0.71 4.83E−02 4 3 LYD339 0.78 2.13E−02 4 6 LYD339 0.80 1.71E−02 4 7 LYD340 0.71 4.67E−02 1 8 LYD340 0.73 4.13E−02 4 3 LYD340 0.71 4.64E−02 4 7 LYD340 0.84 9.57E−03 5 3 LYD340 0.74 3.42E−02 5 6 LYD340 0.89 3.32E−03 5 7 LYD341 0.86 1.40E−02 2 2 LYD341 0.76 2.91E−02 5 16 LYD341 0.71 5.05E−02 5 17 LYD342 0.71 7.17E−02 2 18 LYD342 0.88 4.16E−03 3 12 LYD342 0.80 1.82E−02 4 13 LYD342 0.74 3.71E−02 5 4 LYD343 0.86 1.21E−02 2 2 LYD343 0.77 2.57E−02 3 4 LYD343 0.72 4.25E−02 3 3 LYD343 0.83 1.12E−02 5 14 LYD343 0.70 5.19E−02 5 13 LYD344 0.77 2.43E−02 1 13 LYD344 0.81 2.69E−02 2 2 LYD344 0.74 3.70E−02 3 3 LYD344 0.86 6.81E−03 5 2 Table 5. Provided are the correlations (R) between the expression levels of yield improving genes and their homologues in tissues [roots, seeds, flower, and leaf; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, and direct yield components [Correlation ID vector (corr.)] under normal condition across Arabidopsis accessions. P = p value.

Example 3 Production of Arabidopsis Transcriptom and High Throughput Correlation Analysis of Normal and Nitrogen Limiting Conditions Using 44K Arabidopsis Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis, the present inventors utilized a Arabidopsis oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. The array oligonucleotide represents about 44,000 Arabidopsis genes and transcripts. To define correlations between the levels of RNA expression with NUE, yield components or vigor related parameters various plant characteristics of 14 different Arabidopsis ecotypes were analyzed. Among them, ten ecotypes encompassing the observed variance were selected for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html].

Experimental Procedures

Two tissues of plants [leaves and stems] growing at two different nitrogen fertilization levels (1.5 mM Nitrogen or 6 mM Nitrogen) were sampled and RNA was extracted as described hereinabove under “GENERAL EXPERIMENTAL AND BIOINFORMATICS METHODS”. For convenience, each micro-array expression information tissue type has received a Set ID as summarized in Table 6 below.

TABLE 6 Tissues used for Arabidopsis transcriptom expression sets Expression Set Set ID Leaves at 1.5 mM Nitrogen fertilization 1 Stems at 6 mM Nitrogen fertilization 2 Leaves at 6 mM Nitrogen fertilization 3 Stems at 1.5 mM Nitrogen fertilization 4 Table 6: Provided are the identification (ID) digits of each of the Arabidopsis expression sets.

Assessment of Arabidopsis yield components and vigor related parameters under different nitrogen fertilization levels—10 Arabidopsis accessions in 2 repetitive plots each containing 8 plants per plot were grown at greenhouse. The growing protocol used was as follows: surface sterilized seeds were sown in Eppendorf tubes containing 0.5×Murashige-Skoog basal salt medium and grown at 23° C. under 12-hour light and 12-hour dark daily cycles for 10 days. Then, seedlings of similar size were carefully transferred to pots filled with a mix of perlite and peat in a 1:1 ratio. Constant nitrogen limiting conditions were achieved by irrigating the plants with a solution containing 1.5 mM inorganic nitrogen in the form of KNO₃, supplemented with 2 mM CaCl₂, 1.25 mM KH₂PO₄, 1.50 mM MgSO₄, 5 mM KCl, 0.01 mM H₃BO₃ and microelements, while normal irrigation conditions (Normal Nitrogen conditions) was achieved by applying a solution of 6 mM inorganic nitrogen also in the form of KNO₃, supplemented with 2 mM CaCl₂, 1.25 mM KH₂PO₄, 1.50 mM MgSO₄, 0.01 mM H₃BO₃ and microelements. To follow plant growth, trays were photographed the day nitrogen limiting conditions were initiated and subsequently every 3 days for about 15 additional days. Rosette plant area was then determined from the digital pictures. ImageJ software was used for quantifying the plant size from the digital pictures [Hypertext Transfer Protocol://rsb (dot) info (dot) nih (dot) gov/ij] utilizing proprietary scripts designed to analyze the size of rosette area from individual plants as a function of time. The image analysis system included a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.37 (Java based image processing program, which was developed at the U.S. National Institutes of Health and freely available on the internet [Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute).

Data parameters collected are summarized in Table 7, herein below.

TABLE 7 Arabidopsis correlated parameters (vectors) Correlation Correlated parameter with ID N 6 mM; Seed Yield [gr./plant] 1 N 6 mM; Harvest Index (ratio) 2 N 6 mM; 1000 Seeds weight [gr.] 3 N 6 mM; seed yield/rosette area day at day 10 4 [gr./cm²] N 6 mM; seed yield/leaf blade [gr./cm²] 5 N 1.5 mM; Rosette Area at day 8 [cm^(2]) 6 N 1.5 mM; Rosette Area at day 10 [cm²] 7 N 1.5 mM; Leaf Number at day 10 (number) 8 N 1.5 mM; Leaf Blade Area at day 10 [cm²] 9 N 1.5 mM; RGR of Rosette Area at day 3 [cm²/day] 10 N 1.5 mM; t50 Flowering [day] 11 N 1.5 mM; Dry Weight [gr./plant] 12 N 1.5 mM; Seed Yield [gr./plant] 13 N 1.5 mM; Harvest Index (ratio) 14 N 1.5 mM; 1000 Seeds weight [gr.] 15 N 1.5 mM; seed yield/rosette area at day 10 16 [gr./cm²] N 1.5 mM; seed yield/leaf blade [gr./cm²] 17 N 1.5 mM; % Seed yield reduction compared to N 18 6 mM (ratio) N 1.5 mM; % Biomass reduction compared to N 19 6 mM (ratio) N 6 mM; Rosette Area at day 8 [cm²] 20 N 6 mM; Rosette Area at day 10 [cm²] 21 N 6 mM; Leaf Number at day 10 (number) 22 N 6 mM; Leaf Blade Area at day 10 (cm²) 23 N 6 mM; RGR of Rosette Area at day 3 [cm²/gr.] 24 N 6 mM; t50 Flowering [day] 25 N 6 mM; Dry Weight [gr./plant] 26 N 6 mM; N level/DW (SPAD unit/gr. plant) 27 N 6 mM; DW/N level [gr./SPAD unit] 28 N 6 mM; N level/FW (ratio) 29 N 6 mM; Seed yield/N unit [gr./SPAD unit] 30 N 1.5 mM; N level/FW [SPAD unit/gr.] 31 N 1.5 mM; N level/DW [SPAD unit/gr.] 32 N 1.5 mM; DW/N level [gr/SPAD unit] 33 N 1.5 mM; seed yield/N level [gr/SPAD unit] 34 Table 7. Provided are the Arabidopsis correlated parameters (vectors). “N” = Nitrogen at the noted concentrations; “gr.” = grams; “SPAD” = chlorophyll levels; “t50” = time where 50% of plants flowered; “gr./SPAD unit” = plant biomass expressed in grams per unit of nitrogen in plant measured by SPAD. “DW” = Plant Dry Weight; ″FW″ = Plant Fresh weight; “N level/DW” = plant Nitrogen level measured in SPAD unit per plant biomass [gr.]; “DW/N level” = plant biomass per plant [gr.]/SPAD unit; Rosette Area (measured using digital analysis); Plot Coverage at the indicated day [%] (calculated by the dividing the total plant area with the total plot area); Leaf Blade Area at the indicated day [cm²] (measured using digital analysis); RGR (relative growth rate) of Rosette Area at the indicated day [cm²/day]; t50 Flowering [day[(the day in which 50% of plant flower); seed yield/rosette area at day 10 [gr/cm²] (calculated); seed yield/leaf blade [gr/cm²] (calculated); seed yield/N level [gr/SPAD unit] (calculated).

Assessment of NUE, yield components and vigor-related parameters—Ten Arabidopsis ecotypes were grown in trays, each containing 8 plants per plot, in a greenhouse with controlled temperature conditions for about 12 weeks. Plants were irrigated with different nitrogen concentration as described above depending on the treatment applied. During this time, data was collected documented and analyzed. Most of chosen parameters were analyzed by digital imaging.

Digital Imaging—Greenhouse Assay

An image acquisition system, which consists of a digital reflex camera (Canon EOS 400D) attached with a 55 mm focal length lens (Canon EF-S series) placed in a custom made Aluminum mount, was used for capturing images of plants planted in containers within an environmental controlled greenhouse. The image capturing process is repeated every 2-3 days starting at day 9-12 till day 16-19 (respectively) from transplanting.

The image processing system which was used is described in Example 2 above. Images were captured in resolution of 10 Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, image processing output data was saved to text files and analyzed using the JMP statistical analysis software (SAS institute).

Leaf analysis—Using the digital analysis leaves data was calculated, including leaf number, leaf blade area, plot coverage, Rosette diameter and Rosette area.

Relative growth rate area: The relative growth rate area of the rosette and the leaves was calculated according to Formulas VIII and IX, respectively.

Relative growth rate of rosette area=Regression coefficient of rosette area along time course.  Formula VIII:

Relative growth rate of plant leaf number=Regression coefficient of plant leaf number along time course.  Formula IX

Seed yield and 1000 seeds weight—At the end of the experiment all seeds from all plots were collected and weighed in order to measure seed yield per plant in terms of total seed weight per plant (gr.). For the calculation of 1000 seed weight, an average weight of 0.02 grams was measured from each sample, the seeds were scattered on a glass tray and a picture was taken. Using the digital analysis, the number of seeds in each sample was calculated.

Dry weight and seed yield—At the end of the experiment, plant were harvested and left to dry at 30° C. in a drying chamber. The biomass was separated from the seeds, weighed and divided by the number of plants. Dry weight=total weight of the vegetative portion above ground (excluding roots) after drying at 30° C. in a drying chamber.

Harvest Index (seed)—The harvest index was calculated using Formula IV as described above [Harvest Index=Average seed yield per plant/Average dry weight].

T₅₀ days to flowering—Each of the repeats was monitored for flowering date. Days of flowering was calculated from sowing date till 50% of the plots flowered.

Plant nitrogen level—The chlorophyll content of leaves is a good indicator of the nitrogen plant status since the degree of leaf greenness is highly correlated to this parameter. Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed at time of flowering. SPAD meter readings were done on young fully developed leaf. Three measurements per leaf were taken per plot. Based on this measurement, parameters such as the ratio between seed yield per nitrogen unit [seed yield/N level=seed yield per plant [gr.]/SPAD unit], plant DW per nitrogen unit [DW/N level=plant biomass per plant [gr.]/SPAD unit], and nitrogen level per gram of biomass [N level/DW=SPAD unit/plant biomass per plant (gr.)] were calculated.

Percent of seed yield reduction-measures the amount of seeds obtained in plants when grown under nitrogen-limiting conditions compared to seed yield produced at normal nitrogen levels expressed in percentages (%).

Experimental Results

10 different Arabidopsis accessions (ecotypes) were grown and characterized for 37 parameters as described above. The average for each of the measured parameters was calculated using the JMP software (Table 8 and 9 below). Subsequent correlation analysis between the various transcriptom sets (Table 6) and the average parameters was conducted (Table 10).

TABLE 8 Measured parameters in Arabidopsis accessions Ecotype/ Corr. ID Line-1 Line-2 Line-3 Line-4 Line-5 1 0.11575 0.1651625 0.10846875 0.08195 0.11918125 2 0.27999946 0.30852795 0.28360337 0.15835749 0.2058752 3 0.01474256 0.01686869 0.01776982 0.01207785 0.01553451 4 0.08243942 0.10579199 0.04051086 0.03389743 0.05563382 5 0.33919761 0.52646 0.20718176 0.18267073 0.27723756 6 0.76004675 0.70878892 1.06135087 1.1569617 1.0001808 7 1.42963825 1.32500951 1.7662424 1.97095367 1.83234886 8 6.875 7.3125 7.3125 7.875 7.75 9 0.33486516 0.26631535 0.37431832 0.3868142 0.3699387 10 0.63055011 0.7927894 0.50199713 0.49086784 0.71950821 11 15.9674256 20.967741 14.8356433 24.7083342 23.6981965 12 0.164375 0.12375 0.081875 0.113125 0.12375 13 0.0317625 0.02526875 0.0230125 0.0098375 0.00879375 14 0.19221006 0.20271686 0.29498642 0.08498642 0.07117143 15 0.0164661 0.01575586 0.01752601 0.01428241 0.02237168 16 0.0221105 0.0190193 0.01356505 0.00522479 0.00495957 17 0.09480609 0.09462778 0.06338215 0.02639571 0.02415312 18 72.55939525 84.70067358 78.78421204 87.9957291 92.62153233 19 60.74626866 76.70588235 78.55973813 78.14009662 78.6407767 20 0.75895075 0.85681934 1.4770776 1.27750001 1.09516034 21 1.40594707 1.57034299 2.67253089 2.41758766 2.14203082 22 6.25 7.3125 8.0625 8.75 8.75 23 0.34248457 0.31479663 0.52295373 0.44862141 0.42970295 24 0.6891365 1.02385276 0.61434467 0.60098475 0.65076159 25 16.3714019 20.5000004 14.6346459 24 23.5950703 26 0.41875 0.53125 0.381875 0.5175 0.579375 27 22.49 28.27 28 0.018620067 0.018306704 29 53.70549848 54.62479871 30 0.004209091 0.002952562 31 45.59 42.11 32 167.3003802 241.0607735 33 0.005977273 0.004148331 34 0.001155 0.000360744 Table 8: Provided are the values of each of the parameters measured in Arabidopsis ecotypes (lines 1-5) using the correlation ID numbers described in Table 7 hereinabove.

TABLE 9 Measured parameters in Arabidopsis accessions-continue Ecotype/ Corr. ID Line-6 Line-7 Line-8 Line-9 Line-10 1 0.13876875 0.10695625 0.1380875 0.0948125 0.06754375 2 0.2762645 0.17062181 0.21248036 0.1655574 0.13618211 3 0.01543419 0.01403759 0.01660137 0.01608078 0.01601005 4 0.05702681 0.05537429 0.05071512 0.05818119 0.03071849 5 0.28118206 0.25233196 0.27125843 0.23547195 0.15792361 6 0.91049714 0.94164552 1.11820707 0.63830722 0.99598092 7 1.81767559 1.63622587 1.99606088 1.14962099 1.75392334 8 7.625 7.1875 8.625 5.92857143 7.9375 9 0.38633196 0.34966412 0.37896098 0.30665846 0.37272108 10 0.82522726 0.64561797 0.66798775 0.63647393 0.60534304 11 18.0593189 19.488184 23.5678247 21.8884261 23.5662586 12 0.134375 0.10625 0.148125 0.17125 0.18375 13 0.03231875 0.01931875 0.0120125 0.01350446 0.005525 14 0.24052391 0.1786763 0.08141143 0.07930284 0.03089076 15 0.0147897 0.01364492 0.0216896 0.01860767 0.01834821 16 0.01780867 0.01273805 0.00676616 0.01177002 0.00315298 17 0.08363306 0.05886 0.03430777 0.04403838 0.01485086 18 76.71035446 81.93770818 91.30080565 85.75666711 91.82011659 19 73.19201995 83.06772908 77.18960539 70.11995638 62.97229219 20 1.23563711 1.09369169 1.40984007 0.89057621 1.22408964 21 2.4744351 1.96527638 2.72071991 1.64211359 2.20715087 22 8.375 7.125 9.4375 6.3125 8.0625 23 0.49679143 0.42802388 0.50868963 0.40531471 0.43015889 24 0.67559702 0.58421861 0.61299718 0.51546854 0.47694692 25 15.032695 19.7496866 22.8871401 18.8041534 23.3779994 26 0.50125 0.6275 0.649375 0.573125 0.49625 27 33.32 39 17.64 28 0.015042326 0.014694282 0.028130951 29 66.4790786 68.05368458 35.54803406 30 0.005298764 0.003255054 0.00233267 31 53.11 67 28.15 32 194.9767442 169.3430657 157.8231293 33 0.005128817 0.005905172 0.006336207 34 0.00123354 0.000465671 0.000190517 Table 9: Provided are the values of each of the parameters measured in Arabidopsis ecotypes (lines 6-10) using the correlation ID numbers described in Table 7 hereinabove.

TABLE 10 Correlation between the expression level of selected genes of some embodiments of the invention in various tissues and the phenotypic performance under normal or abiotic stress conditions across Arabidopsis accessions Gene Exp. Corr. Gene Exp. Corr. Name R P value set ID Name R P value set ID LYD289 0.74 1.36E−02 1 19 LYD289 0.72 2.76E−02 2 19 LYD289 0.76 1.02E−02 3 19 LYD289 0.71 2.17E−02 4 19 LYD290 0.78 8.04E−03 1 2 LYD290 0.70 2.34E−02 1 1 LYD290 0.74 1.53E−02 3 20 LYD290 0.81 4.63E−03 3 9 LYD290 0.77 9.60E−03 3 21 LYD290 0.86 1.41E−03 3 23 LYD291 0.74 2.25E−02 2 2 LYD291 0.79 1.13E−02 2 16 LYD291 0.73 2.44E−02 2 4 LYD291 0.81 8.40E−03 2 17 LYD291 0.71 3.28E−02 2 14 LYD291 0.76 1.10E−02 3 16 LYD291 0.76 1.08E−02 3 13 LYD292 0.74 1.38E−02 3 16 LYD292 0.73 1.65E−02 3 17 LYD292 0.75 1.17E−02 3 13 LYD292 0.92 2.05E−04 3 14 LYD293 0.82 3.60E−03 1 11 LYD293 0.77 8.67E−03 1 25 LYD293 0.81 4.43E−03 1 18 LYD293 0.86 2.95E−03 2 8 LYD294 0.71 2.05E−02 1 2 LYD294 0.84 2.53E−03 1 16 LYD294 0.85 1.76E−03 1 17 LYD294 0.84 2.49E−03 1 13 LYD294 0.75 1.18E−02 1 14 LYD294 0.70 2.41E−02 3 2 LYD294 0.72 1.94E−02 3 17 LYD294 0.81 4.93E−03 3 13 LYD295 0.93 8.65E−05 1 11 LYD295 0.89 5.39E−04 1 25 LYD295 0.87 1.15E−03 1 18 LYD295 0.73 1.76E−02 3 25 LYD296 0.71 2.28E−02 1 23 LYD297 0.73 1.58E−02 1 16 LYD297 0.78 7.28E−03 1 13 LYD300 0.73 2.51E−02 2 22 LYD303 0.70 2.39E−02 1 17 LYD303 0.72 1.91E−02 1 13 LYD303 0.77 9.48E−03 3 2 LYD303 0.76 1.11E−02 3 17 LYD303 0.83 2.91E−03 3 13 LYD303 0.73 1.73E−02 3 14 LYD304 0.70 2.34E−02 1 14 LYD304 0.72 1.84E−02 3 24 LYD308 0.78 8.33E−03 4 6 LYD309 0.72 1.82E−02 1 20 LYD310 0.76 1.10E−02 1 20 LYD310 0.73 1.65E−02 1 21 LYD310 0.72 1.82E−02 1 23 LYD315 0.88 8.81E−04 1 2 LYD315 0.82 3.42E−03 1 16 LYD315 0.84 2.10E−03 1 17 LYD315 0.84 2.42E−03 1 13 LYD315 0.79 6.32E−03 1 14 LYD315 0.70 3.57E−02 2 2 LYD315 0.70 3.52E−02 2 13 LYD315 0.79 1.05E−02 2 14 LYD315 0.78 7.74E−03 3 16 LYD315 0.86 1.43E−03 3 4 LYD315 0.75 1.22E−02 3 17 LYD315 0.75 1.33E−02 3 5 LYD315 0.91 2.42E−04 4 2 LYD315 0.75 1.27E−02 4 16 LYD315 0.78 7.43E−03 4 17 LYD315 0.77 9.03E−03 4 13 LYD315 0.81 4.26E−03 4 14 LYD318 0.78 7.45E−03 1 2 LYD318 0.86 1.26E−03 1 1 LYD318 0.75 1.22E−02 1 5 LYD318 0.86 1.36E−03 1 24 LYD318 0.71 2.14E−02 3 16 LYD318 0.74 1.35E−02 3 17 LYD318 0.77 9.45E−03 3 1 LYD318 0.76 1.01E−02 3 13 LYD318 0.72 1.95E−02 3 14 LYD319 0.74 1.41E−02 4 15 LYD320 0.81 4.38E−03 1 2 LYD320 0.76 1.10E−02 1 13 LYD320 0.79 6.15E−03 1 14 LYD320 0.72 2.73E−02 2 2 LYD320 0.81 8.30E−03 2 4 LYD320 0.79 1.20E−02 2 5 LYD320 0.78 1.33E−02 2 24 LYD320 0.78 8.46E−03 3 2 LYD320 0.78 8.03E−03 4 13 LYD320 0.90 3.95E−04 4 14 LYD322 0.72 1.91E−02 1 11 LYD322 0.74 1.43E−02 1 18 LYD323 0.72 1.95E−02 3 2 LYD325 0.86 1.24E−03 3 11 LYD325 0.87 1.22E−03 3 25 LYD325 0.94 6.39E−05 3 18 LYD327 0.79 6.01E−03 1 2 LYD327 0.83 2.81E−03 1 16 LYD327 0.81 4.37E−03 1 17 LYD327 0.92 1.95E−04 1 13 LYD327 0.81 4.43E−03 1 14 LYD327 0.83 5.30E−03 2 14 LYD327 0.80 5.34E−03 4 2 LYD327 0.84 2.31E−03 4 16 LYD327 0.84 2.56E−03 4 17 LYD327 0.92 1.27E−04 4 13 LYD327 0.90 3.59E−04 4 14 LYD330 0.75 2.05E−02 2 3 LYD331 0.74 1.36E−02 1 22 LYD331 0.81 4.46E−03 1 20 LYD331 0.70 2.28E−02 1 6 LYD331 0.81 4.34E−03 1 21 LYD331 0.70 2.39E−02 1 7 LYD331 0.77 9.77E−03 1 23 LYD331 0.75 1.92E−02 2 19 LYD331 0.78 1.34E−02 2 20 LYD331 0.76 1.78E−02 2 21 LYD331 0.71 3.20E−02 2 23 LYD331 0.74 1.36E−02 3 20 LYD331 0.74 1.35E−02 3 21 LYD331 0.87 1.02E−03 4 19 LYD332 0.86 1.42E−03 1 16 LYD332 0.82 3.66E−03 1 17 LYD332 0.90 3.17E−04 1 13 LYD332 0.79 6.66E−03 1 14 LYD332 0.81 4.49E−03 4 16 LYD332 0.80 4.97E−03 4 17 LYD332 0.79 6.44E−03 4 13 LYD334 0.73 2.65E−02 2 6 LYD335 0.71 2.19E−02 1 2 LYD335 0.79 6.85E−03 1 16 LYD335 0.78 8.37E−03 1 17 LYD335 0.73 1.70E−02 1 13 LYD335 0.72 1.85E−02 1 14 LYD335 0.72 1.97E−02 3 1 LYD337 0.76 1.07E−02 4 4 LYD337 0.77 9.01E−03 4 5 LYD339 0.71 2.23E−02 3 10 LYD339 0.78 8.08E−03 3 26 LYD340 0.77 9.66E−03 3 18 LYD340 0.85 1.69E−03 3 15 LYD341 0.76 1.10E−02 3 20 LYD341 0.78 7.19E−03 3 21 LYD341 0.85 1.62E−03 3 23 LYD344 0.80 5.20E−03 1 14 LYD344 0.74 1.49E−02 3 14 Table 10. Provided are the correlations (R) between the expression levels of yield improving genes and their homologues in tissues [Leaves or stems; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.)] under stress conditions or normal conditions across Arabidopsis accessions. P = p value.

Example 4 Production of Tomato Transcriptom and High Throughput Correlation Analysis Using 44K Tomato Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis between NUE related phenotypes and gene expression, the present inventors utilized a Tomato oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. The array oligonucleotide represents about 44,000 Tomato genes and transcripts. In order to define correlations between the levels of RNA expression with NUE, ABST, yield components or vigor related parameters various plant characteristics of 18 different Tomato varieties were analyzed. Among them, 10 varieties encompassing the observed variance were selected for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html].

Correlation of Tomato varieties across ecotypes grown under low Nitrogen, drought and regular growth conditions

Experimental Procedures

10 Tomato varieties were grown in 3 repetitive blocks, each containing 6 plants per plot were grown at net house. Briefly, the growing protocol was as follows:

1. Regular growth conditions: Tomato varieties were grown under normal conditions (4-6 Liters/m² of water per day and fertilized with NPK as recommended in protocols for commercial tomato production).

2. Low Nitrogen fertilization conditions: Tomato varieties were grown under normal conditions (4-6 Liters/m² per day and fertilized with NPK as recommended in protocols for commercial tomato production) until flower stage. At this time, Nitrogen fertilization was stopped.

3. Drought stress: Tomato variety was grown under normal conditions (4-6 Liters/m² per day) until flower stage. At this time, irrigation was reduced to 50% compared to normal conditions. Plants were phenotyped on a daily basis following the standard descriptor of tomato (Table 12). Harvest was conducted while 50% of the fruits were red (mature). Plants were separated to the vegetative part and fruits, of them, 2 nodes were analyzed for additional inflorescent parameters such as size, number of flowers, and inflorescent weight. Fresh weight of all vegetative material was measured. Fruits were separated to colors (red vs. green) and in accordance with the fruit size (small, medium and large). Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute). Data parameters collected are summarized in Tables 13-15, herein below.

Analyzed Tomato tissues—Two tissues at different developmental stages [flower and leaf], representing different plant characteristics, were sampled and RNA was extracted as described above. For convenience, each micro-array expression information tissue type has received a Set ID as summarized in Table 11 below.

TABLE 11 Tomato transcriptom expression sets Expression Set Set ID Leaf at reproductive stage under NUE conditions  1 + 10 Flower under normal conditions 5 + 2 Leaf at reproductive stage under normal conditions 8 + 3 Flower under drought conditions 9 + 7 Leaf at reproductive stage under drought conditions 11 + 4  Flower under NUE conditions 12 + 6  Table 11: Provided are the identification (ID) digits of each of the tomato expression sets.

Table 12 provides the tomato correlated parameters (Vectors). The average for each of the measured parameters was calculated using the JMP software and values are summarized in Tables 13-15 below. Subsequent correlation analysis was conducted. Results were integrated to the database (Table 16).

TABLE 12 Tomato correlated parameters (vectors) Correlation Correlated parameter with ID NUE [yield/SPAD] (Normal) 1 NUpE [biomass/SPAD] (Normal) 2 HI [yield/yield + biomass] (Normal) 3 NUE2 [total biomass/SPAD] (Normal) 4 Total Leaf Area [cm²] (Normal) 5 Leaflet Length [cm] (Normal) 6 Leaflet Width (Normal) 7 100 weight green fruit (Normal) 8 100 weight red fruit (Normal) 9 SLA [leaf area/plant biomass] (Normal) 10 Yield/total leaf area (Normal) 11 Yield/SLA (Normal) 12 Fruit Yield/Plant (NUE) 13 FW/Plant (NUE) 14 average red fruit weight (NUE) 15 Fruit NUE/Normal 16 FW NUE/Normal 17 SPAD NUE 18 RWC NUE 19 SPAD 100% RWC (NUE) 20 SPAD NUE/Normal 21 SAPD 100% RWC NUE/Normal 22 RWC NUE/Normal 23 No flowers (NUE) 24 Weight clusters (flowers) (NUE) 25 Num. Flowers NUE/Normal 26 Cluster Weight NUE/Normal 27 RWC Drought 28 RWC Drought/Normal 29 Num of flowers (Drought) 30 Weight flower clusters (Drought) 31 Num of Flower Drought/Normal 32 Num of Flower Drought/NUE 33 flower cluster weight Drought/Normal 34 flower cluster weight Drought/NUE 35 Fruit Yield/Plant Drought 36 FW/Plant Drought 37 average red fruit weight Drought 38 Fruit Yield Drought/Normal 39 Fruit Drought/NUE 40 FW drought/Normal 41 red fruit weight Drought/Normal 42 Fruit yield/Plant (Normal) 43 FW/Plant (Normal) 44 average red fruit weight (Normal) 45 SPAD (Normal) 46 RWC (Normal) 47 SPAD 100% RWC (Normal) 48 No flowers (Normal) 49 Weight Flower clusters (Normal) 50 Total Leaf Area [cm²]) (Drought) 51 Leaflet Length [cm]) (Drought) 52 Leaflet Width [cm] (Drought) 53 100 weight green fruit (Drought) 54 100 weight red fruit (Drought) 55 NUE [yield/SPAD] (Low N) 56 NUpE [biomass/SPAD] (Low N) 57 HI [yield/yield + biomass] (Low N) 58 NUE2 [total biomass/SPAD] (Low N) 59 Total Leaf Area [cm²] (Low N) 60 Leaflet Length [cm] (Low N) 61 Leaflet Width (Low N) 62 100 weight green fruit (Low N) 63 SLA [leaf area/plant biomass] (Low N) 64 Yield/total leaf area (Low N) 65 Yield/SLA (Low N) 66 100 weight red fruit (Low N) 67 Table 12. Provided are the tomato correlated parameters, “gr.” = grams; “FW” = fresh weight; “NUE” = nitrogen use efficiency; “RWC” = relative water content; “NUpE” = nitrogen uptake efficiency; “SPAD” = chlorophyll levels; “HI” = harvest index (vegetative weight divided on yield); “SLA” = specific leaf area (leaf area divided by leaf dry weight), Treatment in the parenthesis.

Fruit Weight (grams)—At the end of the experiment [when 50% of the fruits were ripe (red)] all fruits from plots within blocks A-C were collected. The total fruits were counted and weighted. The average fruits weight was calculated by dividing the total fruit weight by the number of fruits.

Plant vegetative Weight (grams)—At the end of the experiment [when 50% of the fruit were ripe (red)] all plants from plots within blocks A-C were collected. Fresh weight was measured (grams).

Inflorescence Weight (grams)—At the end of the experiment [when 50% of the fruits were ripe (red)] two Inflorescence from plots within blocks A-C were collected. The Inflorescence weight (gr.) and number of flowers per inflorescence were counted.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed at time of flowering. SPAD meter readings were done on young fully developed leaf. Three measurements per leaf were taken per plot.

Water use efficiency (WUE)—can be determined as the biomass produced per unit transpiration. To analyze WUE, leaf relative water content was measured in control and transgenic plants. Fresh weight (FW) was immediately recorded; then leaves were soaked for 8 hours in distilled water at room temperature in the dark, and the turgid weight (TW) was recorded. Total dry weight (DW) was recorded after drying the leaves at 60° C. to a constant weight. Relative water content (RWC) was calculated according to the following Formula I [(FW−DW/TW−DW)×100] as described above.

Plants that maintain high relative water content (RWC) compared to control lines were considered more tolerant to drought than those exhibiting reduced relative water content.

Experimental Results

TABLE 13 Measured parameters in Tomato accessions (lines 1-6) Ecotype/ Correlation ID No. Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 1 0.02 0.01 0.01 0.00 0.01 0.01 2 0.03 0.09 0.05 0.02 0.05 0.05 3 0.35 0.10 0.14 0.12 0.18 0.19 4 0.05 0.09 0.06 0.02 0.06 0.06 5 426.10 582.38 291.40 593.58 6 6.34 7.99 5.59 7.70 7 3.69 4.77 3.43 4.56 8 0.56 3.05 0.24 2.58 9 0.82 2.46 0.50 2.76 10 140.99 689.67 130.22 299.12 11 0.00 0.00 0.00 0.00 12 0.00 0.00 0.00 0.00 13 0.41 0.66 0.48 0.46 1.35 0.35 14 4.04 1.21 2.25 2.54 1.85 3.06 15 0.02 0.19 0.01 0.01 0.10 0.00 16 0.49 1.93 0.97 3.80 2.78 0.78 17 2.65 0.38 0.74 3.01 0.83 1.54 18 38.40 39.40 47.50 37.00 44.60 41.70 19 74.07 99.08 69.49 63.24 77.36 77.91 20 28.47 39.04 33.01 23.42 34.53 32.51 21 0.77 1.06 0.85 0.80 0.93 0.96 22 0.79 1.37 0.92 0.75 1.31 0.97 23 1.02 1.30 1.08 0.94 1.41 1.00 24 19.00 5.33 9.00 13.00 10.67 16.67 25 0.53 0.37 0.31 0.35 0.47 0.25 26 3.35 0.28 1.42 1.70 1.10 2.00 27 0.46 1.07 0.44 0.01 1.08 0.02 28 72.12 74.51 65.33 72.22 66.13 68.33 29 0.99 0.97 1.02 1.08 1.21 0.88 30 16.67 6.50 15.67 20.33 11.67 25.33 31 0.37 0.41 0.33 0.29 0.55 0.31 32 2.94 0.34 2.47 2.65 1.21 3.04 33 0.88 1.22 1.74 1.56 1.09 1.52 34 0.32 1.19 0.47 0.01 1.25 0.03 35 0.69 1.11 1.06 0.82 1.16 1.25 36 0.47 0.48 0.63 0.35 2.04 0.25 37 2.62 1.09 1.85 2.22 2.63 2.71 38 0.01 0.19 0.21 0.00 0.10 0.00 39 0.57 1.41 1.27 2.88 4.20 0.55 40 1.15 0.73 1.32 0.76 1.51 0.71 41 1.72 0.34 0.61 2.63 1.18 1.36 42 0.19 24.37 25.38 0.02 20.26 0.04 43 0.83 0.34 0.49 0.12 0.49 0.45 44 1.53 3.17 3.02 0.84 2.24 1.98 45 0.05 0.01 0.01 0.29 0.01 0.05 46 49.70 37.20 55.80 46.40 48.20 43.40 47 72.83 76.47 64.29 67.07 54.79 77.61 48 36.17 28.45 35.89 31.09 26.38 33.68 49 5.67 19.33 6.33 7.67 9.67 8.33 50 1.17 0.34 0.69 56.35 0.44 11.31 56 0.01 0.02 0.01 0.02 0.04 0.01 57 0.14 0.03 0.07 0.11 0.05 0.09 58 0.09 0.35 0.18 0.15 0.42 0.10 59 0.16 0.05 0.08 0.13 0.09 0.11 60 565.93 384.77 294.83 378.00 476.39 197.08 61 6.40 5.92 3.69 5.43 6.95 3.73 62 3.47 1.97 1.79 2.55 3.52 1.73 63 0.87 3.66 0.57 0.37 3.40 0.68 64 140.04 317.12 131.29 148.82 257.51 64.34 65 0.00 0.00 0.00 0.00 0.00 0.00 66 0.00 0.00 0.00 0.00 0.01 0.01 67 1.06 6.87 0.65 0.53 7.17 0.44 Table 13. Provided are the values of each of the parameters (as described above in Table 12) measured in tomato accessions (Line number) under all growth conditions. Growth conditions are specified in the experimental procedure section.

TABLE 14 Measured parameters in Tomato accessions (lines 7-12) Ecotype/ Correlation ID No. Line-7 Line-8 Line-9 Line-10 Line-11 Line-12 1 0.01 0.01 0.00 0.01 0.02 0.00 2 0.02 0.04 0.05 0.05 0.05 0.08 3 0.38 0.17 0.06 0.10 0.27 0.05 4 0.03 0.05 0.06 0.06 0.06 0.08 5 947.59 233.35 340.73 339.11 190.14 421.79 6 7.85 6.22 6.16 5.65 4.39 4.44 7 4.44 3.15 3.37 3.13 2.40 2.02 8 6.32 5.75 0.38 0.30 1.95 2.53 9 5.32 5.24 0.61 0.66 2.70 0.70 10 1117.74 111.77 106.29 123.14 104.99 111.88 11 0.00 0.00 0.00 0.00 0.00 0.00 12 0.00 0.00 0.00 0.00 0.01 0.00 13 0.01 0.51 0.44 0.47 1.59 0.39 14 3.13 2.54 1.84 1.52 1.91 1.86 15 0.01 0.01 0.01 0.01 0.02 0.01 16 0.02 1.16 2.07 1.51 2.41 2.06 17 3.70 1.22 0.58 0.55 1.06 0.49 18 34.40 50.00 44.70 53.70 35.70 58.80 19 80.49 67.40 67.16 66.07 69.57 69.30 20 27.66 33.68 30.04 35.50 24.81 40.77 21 0.80 0.94 0.76 1.05 0.89 1.24 22 1.11 0.95 0.79 0.92 0.94 1.36 23 1.38 1.01 1.04 0.88 1.05 1.10 24 6.00 16.00 15.00 6.00 17.00 13.00 25 0.29 0.47 0.40 0.30 0.82 0.40 26 1.20 1.92 1.50 0.86 1.89 1.63 27 0.37 0.81 0.55 0.36 0.95 0.80 28 78.13 18.46 73.21 62.50 67.21 75.76 29 1.34 0.28 1.13 0.83 1.01 1.20 30 29.73 17.33 14.67 29.67 15.00 10.33 31 0.45 0.56 0.30 0.31 0.31 0.31 32 5.95 2.08 1.47 4.24 1.67 1.29 33 4.96 1.08 0.98 4.94 0.88 0.79 34 0.56 0.96 0.42 0.38 0.36 0.62 35 1.52 1.19 0.76 1.04 0.38 0.78 36 0.05 0.45 0.29 1.02 0.60 0.49 37 3.41 2.11 1.95 1.76 1.72 1.92 38 0.03 0.01 0.01 0.00 0.01 0.01 39 0.09 1.03 1.39 3.28 0.91 2.62 40 5.06 0.89 0.67 2.17 0.38 1.27 41 4.02 1.01 0.61 0.64 0.95 0.51 42 0.15 0.02 0.86 0.74 0.09 1.72 43 0.53 0.44 0.21 0.31 0.66 0.19 44 0.85 2.09 3.21 2.75 1.81 3.77 45 0.23 0.29 0.01 0.01 0.06 0.01 46 42.90 53.30 58.50 51.10 40.00 47.60 47 58.18 66.51 64.71 75.25 66.23 63.21 48 24.98 35.47 37.87 38.43 26.49 30.07 49 5.00 8.33 10.00 7.00 9.00 8.00 50 0.79 0.58 0.73 0.83 0.86 0.50 51 337.63 52 5.15 53 2.55 54 0.80 55 0.89 56 0.00 0.02 0.01 0.01 0.06 0.01 57 0.11 0.08 0.06 0.04 0.08 0.05 58 0.00 0.17 0.19 0.24 0.45 0.17 59 0.11 0.09 0.08 0.06 0.14 0.06 60 453.24 625.51 748.01 453.96 164.85 338.30 61 4.39 6.72 6.66 4.39 3.90 5.29 62 1.87 3.54 3.28 2.52 2.61 2.61 63 0.45 0.47 0.54 0.39 0.97 0.91 64 144.60 246.05 405.55 299.32 86.19 182.32 65 0.00 0.00 0.00 0.00 0.01 0.00 66 0.00 0.00 0.00 0.00 0.02 0.00 67 0.55 0.75 0.58 1.27 1.34 Table 14. Provided are the values of each of the parameters (as described above in Table 12) measured in tomato accessions (Line number) under all growth conditions. Growth conditions are specified in the experimental procedure section.

TABLE 15 Measured parameters in Tomato accessions (lines 13-18) Ecotype/ Correlation ID No. Line-13 Line-14 Line-15 Line-16 Line-17 Line-18 1 0.01 0.01 0.01 0.01 0.01 0.00 2 0.03 0.04 0.05 0.03 0.07 0.04 3 0.31 0.12 0.14 0.17 0.09 0.11 4 0.05 0.05 0.06 0.04 0.08 0.04 5 581.33 807.51 784.06 351.80 255.78 1078.10 6 6.77 7.42 6.71 5.87 4.16 10.29 7 3.80 3.74 2.98 3.22 2.09 5.91 8 1.42 2.03 1.39 2.27 0.45 0.42 9 2.64 4.67 2.17 0.49 0.34 0.75 10 307.95 419.37 365.81 212.93 84.94 469.87 11 0.00 0.00 0.00 0.00 0.00 0.00 12 0.00 0.00 0.00 0.00 0.00 0.00 13 0.32 0.45 0.14 0.40 1.44 0.50 14 2.47 2.62 1.08 1.17 0.92 1.09 15 0.01 0.05 0.36 0.04 0.63 16 0.38 1.64 0.41 1.21 4.59 1.70 17 1.31 1.36 0.51 0.71 0.31 0.47 18 47.50 45.20 39.00 45.00 65.30 51.90 19 100.00 57.66 90.79 68.00 59.65 72.17 20 47.47 26.06 35.38 30.60 38.97 37.46 21 0.82 0.94 0.89 0.83 1.57 0.88 22 1.44 1.50 1.05 0.56 1.48 0.84 23 1.76 1.60 1.17 0.68 0.94 0.96 24 8.67 9.33 12.67 6.67 9.33 8.00 25 0.35 0.43 0.35 0.45 0.28 0.47 26 1.63 1.17 1.65 0.74 0.88 0.89 27 0.34 0.61 0.94 0.68 0.40 1.44 28 62.82 70.69 55.75 75.22 63.68 62.31 29 1.11 1.97 0.72 0.75 1.01 0.83 30 18.33 12.00 20.33 12.67 12.67 11.33 31 8.36 0.29 0.34 0.44 0.27 0.43 32 3.44 1.50 2.65 1.41 1.19 1.26 33 2.12 1.29 1.61 1.90 1.36 1.42 34 8.20 0.41 0.91 0.67 0.38 1.31 35 24.12 0.67 0.97 0.99 0.95 0.91 36 0.27 0.68 0.14 0.53 0.55 0.41 37 2.21 3.73 0.75 1.76 0.63 1.11 38 0.00 0.01 0.30 0.14 0.04 0.09 39 0.32 2.48 0.41 1.62 1.76 1.42 40 0.84 1.51 0.98 1.34 0.38 0.84 41 1.17 1.94 0.35 1.06 0.21 0.48 42 0.17 0.02 10.50 27.89 11.79 9.98 43 0.85 0.27 0.35 0.33 0.31 0.29 44 1.89 1.93 2.14 1.65 3.01 2.29 45 0.03 0.26 0.03 0.00 0.00 0.01 46 57.90 48.30 43.60 54.50 41.60 59.10 47 56.77 35.96 77.62 100.00 63.16 75.13 48 32.89 17.35 33.82 54.47 26.25 44.43 49 5.33 8.00 7.67 9.00 10.67 9.00 50 1.02 0.70 0.38 0.66 0.70 0.33 51 130.78 557.93 176.67 791.86 517.05 832.27 52 3.38 7.14 5.48 8.62 6.35 6.77 53 2.04 4.17 3.09 4.69 3.87 2.91 54 0.28 0.38 0.63 2.86 1.16 4.40 55 0.35 0.63 2.27 7.40 2.94 11.60 56 0.01 0.02 0.00 0.01 0.04 0.01 57 0.05 0.10 0.03 0.04 0.02 0.03 58 0.12 0.15 0.12 0.25 0.61 0.31 59 0.06 0.12 0.03 0.05 0.06 0.04 60 396.00 236.15 174.58 441.78 489.18 707.80 61 6.32 5.11 4.72 6.83 7.10 8.21 62 3.58 2.56 2.48 3.43 3.30 3.69 63 0.36 0.35 0.57 4.38 2.02 8.13 64 160.18 90.10 160.99 379.03 531.08 650.68 65 0.00 0.00 0.00 0.00 0.00 0.00 66 0.00 0.00 0.00 0.00 0.00 0.00 67 0.52 0.57 0.94 6.17 3.67 11.33 Table 15: Provided are the values of each of the parameters (as described above in Table 12) measured in tomato accessions (Line number) under all growth conditions. Growth conditions are specified in the experimental procedure section.

TABLE 16 Correlation between the expression level of selected genes of some embodiments of the invention in various tissues and the phenotypic performance under normal and stress conditions across tomato ecotypes Gene Exp. Corr. Gene Exp. Corr. Name R P value set ID Name R P value set ID LYD475 0.71 2.04E−02 1 20 LYD475 0.79 6.15E−03 1 22 LYD475 0.77 2.51E−02 2 12 LYD475 0.75 3.15E−02 2 11 LYD475 0.73 1.61E−02 12 19 LYD477 0.87 9.33E−04 1 20 LYD477 0.88 3.84E−03 2 12 LYD477 0.84 9.63E−03 2 11 LYD477 0.81 4.38E−03 11 35 LYD477 0.80 5.67E−03 11 34 LYD477 0.81 4.78E−03 11 31 LYD478 0.73 1.69E−02 1 20 LYD478 0.83 5.37E−03 2 3 LYD478 0.85 4.01E−03 2 1 LYD478 0.76 2.79E−02 2 9 LYD478 0.88 1.78E−03 3 1 LYD478 0.86 1.59E−03 9 35 LYD478 0.83 2.72E−03 9 34 LYD478 0.85 1.69E−03 9 31 LYD478 0.88 8.98E−04 12 20 LYD478 0.73 1.76E−02 12 23 LYD478 0.82 3.55E−03 12 19 LYD479 0.80 1.76E−02 2 11 LYD479 0.73 1.63E−02 6 59 LYD479 0.75 1.17E−02 6 57 LYD479 0.77 9.70E−03 9 33 LYD479 0.75 1.24E−02 9 30 LYD479 0.74 1.37E−02 12 14 LYD479 0.83 3.23E−03 12 17 LYD479 0.77 8.56E−03 12 26 LYD479 0.71 2.25E−02 11 33 LYD479 0.76 1.10E−02 11 40 LYD480 0.92 4.80E−04 3 3 LYD480 0.81 8.33E−03 3 1 LYD480 0.74 1.36E−02 8 46 LYD481 0.89 1.16E−03 2 3 LYD481 0.94 1.51E−04 2 1 LYD481 0.82 1.18E−02 2 9 LYD481 0.78 1.41E−02 3 4 LYD482 0.73 4.01E−02 2 12 LYD482 0.81 1.41E−02 2 11 LYD482 0.76 1.13E−02 5 46 LYD482 0.72 1.87E−02 11 35 LYD482 0.82 3.41E−03 11 34 LYD482 0.74 1.47E−02 11 31 LYD483 0.77 2.42E−02 2 12 LYD483 0.74 3.73E−02 2 11 LYD483 0.75 1.95E−02 3 3 LYD483 0.83 2.98E−03 8 46 LYD484 0.73 1.63E−02 1 22 LYD484 0.75 1.95E−02 2 3 LYD484 0.81 8.10E−03 2 1 LYD487 0.78 2.17E−02 2 12 LYD487 0.74 2.39E−02 2 3 LYD487 0.75 1.99E−02 2 1 LYD487 0.84 9.32E−03 2 11 LYD489 0.72 2.72E−02 3 3 LYD489 0.90 2.63E−03 2 12 LYD489 0.81 1.44E−02 2 11 LYD489 0.81 4.72E−03 11 42 LYD489 0.83 3.14E−03 11 38 LYD491 0.70 5.16E−02 2 12 LYD491 0.74 3.46E−02 2 11 LYD491 0.74 2.24E−02 3 3 LYD491 0.77 1.55E−02 3 1 LYD491 0.75 1.26E−02 9 35 LYD491 0.78 7.60E−03 9 34 LYD491 0.75 1.31E−02 9 31 LYD491 0.72 1.85E−02 11 34 LYD491 0.71 2.25E−02 11 31 LYD492 0.83 3.20E−03 1 20 LYD492 0.73 1.67E−02 1 23 LYD492 0.71 2.06E−02 1 22 LYD492 0.76 1.07E−02 1 19 LYD492 0.83 5.13E−03 3 3 LYD492 0.80 1.04E−02 3 1 Table 16. Provided are the correlations (R) between the expression levels yield improving genes and their homologs in various tissues [Expression (Exp) sets] and the phenotypic performance [yield, biomass, growth rate and/or vigor components (Correlation vector (Corr.) ID)] under normal conditions across tomato ecotypes. P = p value.

Example 5 Production of B. Juncea Transcriptom and High Throughput Correlation Analysis with Yield Parametrers Using 60K B. Juncea Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis, the present inventors utilized a B. juncea oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. The array oligonucleotide represents about 60,000 B. juncea genes and transcripts. In order to define correlations between the levels of RNA expression with yield components or vigor related parameters, various plant characteristics of 11 different B. juncea varieties were analyzed and used for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test.

Correlation of B. juncea Genes' Expression Levels with Phenotypic Characteristics Across Ecotype

Experimental Procedures

11 B. juncea varieties were grown in three repetitive plots, in field. Briefly, the growing protocol was as follows: B. juncea seeds were sown in soil and grown under normal condition till harvest. In order to define correlations between the levels of RNA expression with yield components or vigor related parameters, the 11 different B. juncea varieties were analyzed and used for gene expression analyses.

TABLE 17 Tissues used for B, juncea transcriptom expression sets Expression Set Set ID Meristem at vegetative stage under normal growth 1 conditions Flower at flowering stage under normal growth conditions 2 Leaf at vegetative stage under normal growth conditions 3 Pod (R1-R3) under normal growth conditions 4 Pod (R4-R5) under normal growth conditions 5 Table 17: Provided are the identification (ID) digits of each of the B, juncea expression sets.

RNA extraction—All 11 selected B. juncea varieties were sample per each treatment. Plant tissues [leaf, Pod, Lateral meristem and flower] growing under normal conditions were sampled and RNA was extracted as described above.

The collected data parameters were as follows:

Fresh weight (plot-harvest) [gr/plant]—total fresh weight per plot at harvest time normalized to the number of plants per plot.

Seed Weight [milligrams/plant]—total seeds from each plot was extracted, weighted and normalized for plant number in each plot.

Harvest index—The harvest index was calculated: seed weight/fresh weight

Days till bolting/flowering—number of days till 50% bolting/flowering for each plot.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed at time of flowering. SPAD meter readings were done on young fully developed leaf. Three measurements per leaf were taken for each plot.

Main branch—average node length—total length/total number of nods on main branch.

Lateral branch—average node length—total length/total number of nods on lateral branch.

Main branch—20th length—the length of the pod on the 20^(th) node from the apex of main branch.

Lateral branch—20th length—the length of the pod on the 20^(th) node from the apex of lateral branch.

Main branch—20th seed No. —number of seeds in the pod on the 20^(t)h node from the apex of main branch.

Lateral branch—20th seed number—number of seeds in the pod on the 20^(t)h node from the apex of lateral branch.

Number of lateral branches—total number of lateral branches, average of three plants per plot.

Main branch height [cm]—total length of main branch.

Min-lateral branch position—lowest node on the main branch that has developed lateral branch.

Max-lateral branch position [#node of main branch]—highest node on the main branch that has developed lateral branch.

Max-number of nodes in lateral branch—the highest number of node that a lateral branch had per plant.

Max length of lateral branch [cm]—the highest length of lateral branch per plant.

Max diameter of lateral branch [mm]—the highest base diameter that a lateral branch had per plant.

Oil Content—Indirect oil content analysis was carried out using Nuclear Magnetic Resonance (NMR) Spectroscopy, which measures the resonance energy absorbed by hydrogen atoms in the liquid state of the sample [See for example, Conway TF. and Earle F R., 1963, Journal of the American Oil Chemists' Society; Springer Berlin/Heidelberg, ISSN: 0003-021X (Print) 1558-9331 (Online)];

Fresh weight (single plant) (gr/plant)—average fresh weight of three plants per plot taken at the middle of the season.

Main branch base diameter [mm]—the based diameter of main branch, average of three plants per plot.

1000 Seeds [gr]—weight of 1000 seeds per plot.

Experimental Results

Eleven different B. juncea varieties (i.e., Lines 1-11) were grown and characterized for 23 parameters as specified in Table 18, below. The average for each of the measured parameters was calculated using the JMP software and values are summarized in Tables 19-20 below. Subsequent correlation analysis between the various transcriptom expression sets and the average parameters was conducted (Table 21). Results were then integrated to the database.

TABLE 18 Measured parameters in B, juncea accessions Correlation Correlated parameter with ID Days till bolting (days) 1 Fresh weight (plot-harvest) [gr./plant] 2 Seed weight per plant (gr.) 3 Harvest index (ratio) 4 Days till flowering (days) 5 SPAD 6 Main branch - average node length (cm) 7 Lateral branch - average node length (cm) 8 Main branch - 20th length (cm) 9 Lateral branch - 20th length (cm) 10 Main branch - 20th seed number (number) 11 Lateral branch - 20th seed number (number) 12 Number of lateral branches (number) 13 Main branch height [cm] 14 Min-Lateral branch position ([No. of node of main branch) 15 Max-Lateral branch position [No. of node of main branch] 16 Max-Number of nodes in lateral branch (number) 17 Max-Length of lateral branch [cm] 18 Max-Diameter of lateral branch [mm] 19 Oil content (mg) 20 Fresh weight (single plant) [gr./plant] 21 Main branch base diameter [mm] 22 1000 Seeds [gr.] 23 Table 18. Provided are the B, juncea correlated parameters, “gr.” = grams; mm = millimeters; “cm” = centimeters; “mg” = milligrams; “SPAD” = chlorophyll levels;

TABLE 19 Measured parameters in B. juncea accessions (lines 1-6) Ecotype/ Correlation ID No. Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 1 57.33 60.33 59.67 56.33 55.00 46.67 2 69.24 45.22 39.27 49.11 43.95 46.42 3 0.00 0.01 0.01 0.01 0.01 0.01 4 0.00 0.00 0.00 0.00 0.00 0.00 5 66.00 69.67 69.33 66.00 61.33 53.00 6 33.02 30.01 32.83 37.53 41.44 35.41 7 0.48 0.41 0.63 0.43 0.38 0.68 8 0.65 0.43 0.74 0.57 0.56 0.79 9 4.28 3.72 3.62 3.50 2.74 5.20 10 4.32 3.69 4.14 3.37 3.06 3.96 11 13.22 13.67 10.44 14.11 9.78 15.22 12 13.00 14.00 13.22 13.44 11.00 13.11 13 15.22 14.89 13.56 14.89 14.00 9.78 14 140.72 125.22 112.44 133.39 142.00 101.50 15 6.78 6.33 5.56 3.67 3.00 3.11 16 15.22 14.89 13.56 14.89 14.00 10.89 17 5.22 7.00 5.22 7.00 6.56 9.44 18 40.44 47.22 41.61 60.50 59.78 59.44 19 4.20 4.85 4.34 5.74 5.87 5.68 20 40.19 40.71 40.91 38.57 40.14 42.63 21 197.78 142.22 147.22 243.33 192.33 163.78 22 14.53 11.99 19.91 14.32 12.59 12.30 23 3.76 2.21 3.26 2.36 2.00 3.12 Table 19: Provided are the values of each of the parameters (as described above) measured in B. juncea accessions (line numbers) under normal conditions.

TABLE 20 Measured parameters in B. juncea accessions (lines 7-11) Ecotype/ Correlation ID No. Line-7 Line-8 Line-9 Line-10 Line-11 1 59.00 54.33 59.67 57.33 53.00 2 36.14 32.58 33.16 63.23 60.94 3 0.00 0.00 0.00 0.01 0.01 4 0.00 0.00 0.00 0.00 0.00 5 69.67 63.67 69.67 71.00 58.33 6 33.17 32.87 34.80 31.82 41.49 7 0.40 0.63 0.57 0.59 1.55 8 0.57 0.76 0.96 0.78 0.90 9 3.91 3.98 3.46 3.73 4.04 10 4.33 4.21 4.14 4.04 3.88 11 12.00 12.67 9.89 11.56 15.56 12 11.89 13.44 11.22 13.22 14.00 13 16.44 14.33 14.56 14.11 16.78 14 145.39 131.56 129.89 131.56 116.44 15 7.78 6.22 5.56 4.89 5.33 16 16.44 14.33 14.56 14.11 16.78 17 6.11 5.22 5.67 6.56 6.00 18 47.28 47.33 44.67 58.67 47.17 19 4.52 4.89 4.68 5.56 5.49 20 41.34 40.82 40.82 38.14 37.21 21 164.44 181.11 176.22 217.89 261.11 22 12.60 12.91 12.56 13.77 13.56 23 3.34 3.09 3.39 3.40 2.39 Table 20: Provided are the values of each of the parameters (as described above) measured in B. juncea accessions (line numbers) under normal conditions.

TABLE 21 Correlation between the expression level of selected genes of some embodiments of the invention in various tissues and the phenotypic performance under normal conditions across B. Juncea accessions Corr. Gene Exp. Corr. Gene Exp. Set Name R P value set Set ID Name R P value set ID LYD346 0.76 6.81E−03 5 20 LYD347 0.84 3.86E−02 2 3 LYD347 0.77 7.40E−02 2 2 LYD347 0.85 3.34E−02 2 12 LYD348 0.70 1.18E−01 2 19 LYD348 0.78 6.45E−02 2 11 LYD348 0.96 2.23E−03 2 21 LYD348 0.89 1.78E−02 2 3 LYD348 0.79 6.14E−02 2 7 LYD348 0.94 6.04E−03 2 2 LYD348 0.77 5.36E−03 5 17 LYD349 0.95 8.71E−05 1 21 LYD349 0.79 6.32E−02 2 21 LYD349 0.97 1.06E−03 2 3 LYD349 0.77 7.19E−02 2 7 LYD349 0.85 3.18E−02 2 2 LYD349 0.74 9.30E−02 2 12 LYD349 0.70 2.40E−02 3 22 LYD349 0.84 1.32E−03 5 8 LYD351 0.86 2.81E−03 1 2 LYD351 0.70 1.20E−01 2 21 LYD351 0.91 1.08E−02 2 3 LYD351 0.92 9.53E−03 2 2 LYD351 0.84 3.73E−02 2 12 LYD351 0.73 1.02E−02 5 7 LYD351 0.71 1.50E−02 5 8 LYD352 0.78 1.24E−02 1 6 LYD352 0.83 5.97E−03 1 21 LYD352 0.78 1.30E−02 1 4 LYD352 0.73 2.45E−02 1 3 LYD352 0.90 1.11E−03 1 7 LYD352 0.72 1.05E−01 2 20 LYD352 0.85 3.11E−02 2 4 LYD353 0.93 3.25E−04 1 11 LYD353 0.71 3.22E−02 1 17 LYD353 0.88 2.07E−02 2 11 LYD353 0.80 5.37E−02 2 21 LYD353 0.84 3.75E−02 2 3 LYD353 0.97 1.03E−03 2 7 LYD354 0.94 4.59E−03 2 3 LYD354 0.72 1.05E−01 2 2 LYD354 0.77 7.17E−02 2 12 LYD354 0.77 1.59E−02 1 17 LYD354 0.74 2.15E−02 1 9 LYD354 0.71 1.39E−02 5 20 LYD354 0.72 1.20E−02 5 9 LYD355 0.85 3.49E−03 1 11 LYD355 0.90 8.14E−04 1 9 LYD355 0.87 2.61E−02 2 21 LYD355 0.95 3.74E−03 2 3 LYD355 0.72 1.07E−01 2 7 LYD355 0.94 5.40E−03 2 2 LYD355 0.79 4.05E−03 5 8 LYD356 0.73 1.68E−02 3 10 LYD356 0.79 7.12E−03 3 23 LYD357 0.92 8.69E−03 2 11 LYD357 0.87 2.54E−02 2 21 LYD357 0.88 2.07E−02 2 3 LYD357 0.98 5.08E−04 2 7 LYD357 0.73 1.02E−01 2 12 LYD357 0.82 3.51E−03 3 4 LYD358 0.86 2.81E−03 1 4 LYD358 0.78 6.49E−02 2 20 LYD358 0.86 2.77E−02 2 4 LYD358 0.88 7.61E−04 3 6 LYD358 0.72 1.29E−02 5 3 LYD359 0.80 5.55E−02 2 6 LYD359 0.78 6.68E−02 2 11 LYD359 0.85 3.12E−02 2 21 LYD359 0.94 5.89E−03 2 3 LYD359 0.90 1.34E−02 2 7 LYD359 0.79 6.11E−03 3 6 LYD360 0.76 1.86E−02 1 4 LYD360 0.70 1.21E−01 2 10 LYD360 0.77 7.03E−02 2 1 LYD360 0.89 1.89E−02 2 23 LYD360 0.82 4.39E−02 2 5 LYD360 0.91 1.14E−02 2 8 LYD360 0.70 1.62E−02 5 4 LYD361 0.91 1.23E−02 2 4 LYD361 0.82 3.94E−03 3 7 LYD361 0.85 1.84E−03 3 8 LYD361 0.76 6.39E−03 5 22 LYD362 0.82 7.41E−03 1 6 LYD362 0.82 6.74E−03 1 7 LYD362 0.78 6.84E−02 2 4 LYD362 0.72 2.00E−02 3 2 LYD364 0.75 1.97E−02 1 23 LYD364 0.77 7.31E−02 2 21 LYD364 0.92 9.20E−03 2 3 LYD364 0.89 1.74E−02 2 2 LYD364 0.72 1.05E−01 2 12 LYD365 0.86 2.66E−02 2 11 LYD365 0.83 3.98E−02 2 9 LYD365 0.84 3.55E−02 2 16 LYD365 0.84 3.55E−02 2 13 LYD366 0.89 1.67E−02 2 11 LYD366 0.90 1.55E−02 2 21 LYD366 0.85 3.10E−02 2 3 LYD366 0.82 4.41E−02 2 7 LYD366 0.91 1.24E−02 2 2 LYD366 0.80 5.80E−02 2 12 LYD367 0.79 1.06E−02 1 7 LYD367 0.74 2.23E−02 1 8 LYD367 0.88 1.92E−02 2 11 LYD367 0.71 1.10E−01 2 21 LYD367 0.80 5.61E−02 2 3 LYD367 0.94 4.77E−03 2 7 LYD367 0.71 2.02E−02 3 6 LYD368 0.78 1.35E−02 1 4 LYD368 0.81 4.99E−02 2 6 LYD368 0.78 6.86E−02 2 21 LYD368 0.73 1.02E−01 2 3 LYD368 0.87 2.58E−02 2 7 LYD368 0.83 1.54E−03 5 23 LYD497 0.81 7.77E−03 1 4 LYD497 0.89 1.60E−02 2 16 LYD497 0.89 1.60E−02 2 13 LYD497 0.71 1.42E−02 5 18 LYD497 0.72 1.21E−02 5 17 LYD498 0.72 2.85E−02 1 7 LYD498 0.94 6.09E−03 2 11 LYD498 0.86 2.92E−02 2 7 LYD498 0.87 2.44E−02 2 16 LYD498 0.87 2.44E−02 2 13 LYD498 0.74 1.54E−02 3 19 LYD498 0.78 7.69E−03 3 18 LYD499 0.71 1.12E−01 2 11 LYD499 0.94 4.67E−03 2 21 LYD499 0.84 3.73E−02 2 3 LYD499 0.80 5.81E−02 2 7 LYD499 0.93 7.27E−03 2 2 LYD500 0.73 1.01E−01 2 20 LYD500 0.78 6.91E−02 2 4 LYD500 0.82 1.96E−03 5 20 LYD501 0.91 6.50E−04 1 7 LYD501 0.95 4.38E−03 2 11 LYD501 0.84 3.49E−02 2 7 LYD501 0.84 3.77E−02 2 9 LYD501 0.91 1.21E−02 2 16 LYD501 0.91 1.21E−02 2 13 LYD501 0.72 1.99E−02 3 21 Table 21. Provided are the correlations (R) between the expression levels of yield improving genes and their homologues in tissues [Leaves, meristem, flower and pods; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.) ID] under normal conditions across B, juncea accessions. P = p value.

Example 6 Production of B. Juncea Transcriptom and High Throughput Correlation Analysis with Yield Parameters of Juncea Grown Under Various Population Densities Using 60K B. Juncea Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis, the present inventors utilized a B. juncea oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. The array oligonucleotide represents about 60,000 B. juncea genes and transcripts. In order to define correlations between the levels of RNA expression with yield components or vigor related parameters, various plant characteristics of two different B. juncea varieties grown under seven different population densities were analyzed and used for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test.

Correlation of B. juncea Genes' Expression Levels with Phenotypic Characteristics Across Seven Population Densities for Two Ecotypes

Experimental Procedures

Two B. juncea varieties were grown in a field under seven population densities (10, 60, 120, 160, 200, 250 and 300 plants per m²) in two repetitive plots. Briefly, the growing protocol was as follows: B. juncea seeds were sown in soil and grown under normal condition till harvest. In order to define correlations between the levels of RNA expression with yield components or vigor related parameters, the two different B. juncea varieties grown under various population densities were analyzed and used for gene expression analyses. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test for each ecotype independently.

TABLE 22 Tissues used for B. juncea transcriptom expression sets Expression Set Set ID Meristem under normal growth conditions various 1 + 2 population densities Flower under normal growth conditions various population 3 densities Table 22: Provided are the identification (ID) digits of each of the B, juncea expression sets.

RNA extraction—the two B. juncea varieties grown under seven population densities were sample per each treatment. Plant tissues [Flower and Lateral meristem] growing under Normal conditions were sampled and RNA was extracted as described above. For convenience, each micro-array expression information tissue type has received a Set ID.

The collected data parameters were as follows:

Fresh weight (plot-harvest) [gr/plant]—total fresh weight per plot at harvest time normalized to the number of plants per plot.

Seed weight [gr/plant]—total seeds from each plot was extracted, weighted and normalized for plant number in each plot.

Harvest index—The harvest index was calculated: seed weight/fresh weight

Days till bolting/flowering—number of days till 50% bolting/flowering for each plot.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed at time of flowering. SPAD meter readings were done on young fully developed leaf. Three measurements per leaf were taken for each plot.

Main branch—average node length—total length/total number of nods on main branch.

Lateral branch—average node length—total length/total number of nods on lateral branch.

Main branch—20th length—the length of the pod on the 20^(th) node from the apex of main branch.

Lateral branch—20th length—the length of the pod on the 20^(th) node from the apex of lateral branch.

Main branch—20th seed No. —number of seeds in the pod on the 20^(t)h node from the apex of main branch.

Lateral branch—20th seed number—number of seeds in the pod on the 20^(t)h node from the apex of lateral branch.

Number of lateral branches—total number of lateral branches, average of three plants per plot.

Main branch height [cm]—total length of main branch.

Min-Lateral branch position—lowest node on the main branch that has developed lateral branch.

Max-Lateral branch position [#node of main branch]—highest node on the main branch that has developed lateral branch.

Max-number of nodes in lateral branch—the highest number of node that a lateral branch had per plant.

Max-length of lateral branch [cm]—the highest length of lateral branch per plant.

Max diameter of lateral branch [mm]—the highest base diameter that a lateral branch had per plant.

Oil content—Indirect oil content analysis was carried out using Nuclear Magnetic Resonance (NMR) Spectroscopy, which measures the resonance energy absorbed by hydrogen atoms in the liquid state of the sample [See for example, Conway TF. and Earle F R., 1963, Journal of the American Oil Chemists' Society; Springer Berlin/Heidelberg, ISSN: 0003-021X (Print) 1558-9331 (Online)];

Fresh weight (single plant) (gr/plant)—average fresh weight of three plants per plot taken at the middle of the season.

Main branch base diameter [mm]—the based diameter of main branch, average of three plants per plot.

1000 Seeds [gr]—weight of 1000 seeds per plot.

Main branch-total number of pods—total number of pods on the main branch, average of three plants per plot.

Main branch-dist. 1-20—the length between the youngest pod and pod number 20 on the main branch, average of three plants per plot.

Lateral branch-total number of pods—total number of pods on the lowest lateral branch, average of three plants per plot.

Lateral branch-dis. 1-20—the length between the youngest pod and pod number 20 on the lowest lateral branch, average of three plants per plot.

Dry weight/plant—weight of total plants per plot at harvest after three days at oven at 60° C. normalized for the number of plants per plot.

Total leaf area—Total leaf area per plot was calculated based on random three plants and normalized for number of plants per plot.

Total Perim. —total perimeter of leaves, was calculated based on random three plants and normalized for number of plants per plot.

Experimental Results

Two B. juncea varieties were grown under seven different population densities and characterized for 30 parameters as specified in Table 23 below. The average for each of the measured parameter was calculated using the JMP software and values are summarized in Tables 24-26 below. Subsequent correlation analysis between the expression of selected genes in various transcriptom expression sets and the average parameters was conducted. Results were then integrated to the database (Table 27).

TABLE 23 Correlation parameters in B, juncea accessions Correlation Correlated parameter with ID Main branch base diameter [mm] 1 Fresh Weight (single plant) [gr./plant] 2 Main branch height [cm] 3 Number of lateral branches (number) 4 Min-Lateral branch position (number of node 5 on the main stem) Max-Lateral branch position (number of node 6 on the main stem) Max-Number of nodes in lateral branch 7 (number) Max-Length of lateral branch [cm] 8 Max-Diameter of lateral branch [mm] 9 Main branch-total number of pods (number) 10 Main branch-dist. 1-20 11 Main branch-20th length (cm) 12 Main branch-20th seed number (number) 13 Lateral branch-total number of pods (number) 14 Lateral branch-dist. 1-20 15 Lateral branch-20th length (cm) 16 Lateral branch-20th seed number (number) 17 Oil content (mg) 18 SPAD 19 days till bolting (days) 20 days till flowering (days) 21 Fresh weight (at harvest)/plant (gr/plant) 22 Dry weight/plant (gr./plant) 23 Seed weight/plant (gr./plant) 24 Fresh weight (harvest)/hectare (Kg/hectare) 25 Dry weight/hectare (Kg./hectare) 26 Seed weight/hectare 27 1000 Seeds [gr.] 28 Total leaf area (cm) 29 Total perim (cm). 30 Table 23. Provided are the B, juncea correlated parameters. “gr.” = grams; mm = millimeters; “cm” = centimeters; “mg” = milligrams; “SPAD” = chlorophyll levels; “Kg.” = kilograms;

TABLE 24 Measured parameters in B. juncea varieties at various population densities Variety at population density/ line line line line line Correlation 1-density: 1-density: 1-density: 1-density: 1-density: ID No. 10 120 160 200 250 1 14.7666667 6.9 5.61666667 4.99166667 6.45 2 0.3675 0.03583333 0.03333333 0.02416667 0.0375 3 118.666667 115.5 111.333333 106 117.5 4 17.1666667 19.1666667 15.8333333 19.3333333 18.333333 5 1 11 7 11 9 6 20 23 19 24 22 7 10 4 4 4 6 8 122 41 43 36 40 9 7.7 2.9 2.5 2 3.4 10 20 15.33333333 17.6666667 16.5 23.166667 11 42.35 27.9 31.2166667 26.05 27.716667 12 5.11666667 4.633333333 4.6 4.66666667 4.7333333 13 20 17.66666667 18 18.5 17.666667 14 17.3333333 11.66666667 10.6666667 10.1666667 12.5 15 40.7333333 17.53333333 19.0833333 15.65 15.233333 16 5.11666667 4.483333333 4.36666667 4.33333333 4.35 17 21.6666667 19.33333333 17 18.8333333 15.666667 18 28.855 29.615 29.57 30.585 29.87 19 43.49 41.95 40.48 37.93 39.5 20 53 50.5 48 53 50 21 67 64 64 64 64 22 0.25972617 0.017544463 0.01160373 0.00941177 0.0086383 23 0.07146015 0.007860795 0.00318829 0.00218658 0.0027891 24 0.02093378 0.001837079 0.00088821 0.00073613 0.0008761 25 22434.188 22067.23763 32929.2929 18596.0411 20654.321 26 6109.01654 9857.366286 8940.69724 4363.21162 6702.2185 27 1797.45096 2307.336938 2552.83939 1466.27328 2100.3779 28 1.80123016 1.7524685 1.62082389 1.98973809 1.9222969 29 508.273183 37.4855833 24.9985 14.33268 50.78652 30 862.832233 100.498267 67.98265 37.90552 97.50658 Table 24: Provided are the values of each of the parameters (as described in Table 23 above) measured in B. juncea 2 varieties at the indicated population densities under normal conditions. For example, “line 1 density: 10” refers to Juncea variety 1 grown at a population density of 10 plants per m².

TABLE 25 Measured parameters in B. juncea varieties at various population densities Variety at population density/ line line line line line Correlation 1-density: 1-density: 2-density: 2-density: 2-density: ID No. 300 60 10 120 160 1 3.95 7.3666667 18.9 7.8083333 6.79166667 2 0.02166667 0.074 0.335 0.0433333 0.03166667 3 108 116 133.166667 144.58333 144.916667 4 17.8333333 16.166667 12.5 15.333333 16.8333333 5 9 5 1 8 9 6 20 20 14 17 21 7 4 6 11 6 5 8 42 78 127 42 34 9 2.5 4.4 8.4 3 2.6 10 16.83333333 15.166667 30.66666667 35.166667 29.83333333 11 31.85 37.583333 38.71666667 32.85 28.76666667 12 4.683333333 5.1 4.666666667 3.85 4.433333333 13 17.5 17.666667 14.33333333 10.333333 13.83333333 14 9.833333333 14 29.83333333 17.333333 12.83333333 15 17.73333333 28.25 33.41666667 14.266667 9.833333333 16 4.4 4.95 4.483333333 3.6666667 3.983333333 17 17.16666667 14.55 12.83333333 10.166667 12.33333333 18 25.215 26.775 34.39 38.65 39.66 19 45.57 40.89 43.83 41.31 40.86 20 51.5 53 55 50.5 47 21 62.5 62.5 64 61 61 22 0.009480434 0.0470682 0.186308744 0.015699 0.013530187 23 0.002374948 0.0111681 0.045443225 0.0045977 0.004239026 24 0.000755044 0.0031703 0.014292085 0.0015562 0.001265508 25 24019.71326 33376.441 16427.35043 15747.619 18531.76931 26 6009.085327 7906.6628 3979.782952 4609.2529 5801.024836 27 1901.668907 2247.0135 1270.039245 1560.5283 1732.849463 28 1.54010747 1.5648537 2.81538106 3.1954331 2.87691722 29 29.1283 76.394583 1338.57912 76.818567 34.4628 30 61.16926 219.13607 1518.31188 162.79095 82.7731667 Table 25: Provided are the values of each of the parameters (as described in Table 23 above) measured in B. juncea 2 varieties at the indicated population densities under normal conditions. For example, “line 2-density: 300” refers to Juncea variety 2 grown at a population density of 300 plants per m².

TABLE 26 Measured parameters in B. juncea varieties at various population densities Variety at popu- lation density/ Cor- line line line line relation 2-density: 2-density: 2-density: 2-density: ID No. 200 250 300 60 1 6.95 7.533333 5.441667 8.766667 2 0.025 0.028333 0.024167 0.065833 3 138.5 144.1667 135.75 157.3333 4 16.66667 16.66667 15.5 12.83333 5 8 10 8 3 6 18 19 18 16 7 4 6 4 11 8 23 38 25 109 9 2.1 2.8 2.35 8 10 30.83333 29.33333 25.33333 33.83333 11 25.3 26.38333 25.06667 45.25 12 4.116667 4.116667 4.233333 4.433333 13 10.33333 11 10.66667 13.16667 14 11.16667 13 9 18.5 15 8.6 10.98333 6.35 21.58333 16 4.033333 3.966667 3.7 4.716667 17 10.66667 9.833333 9 11.16667 18 36.795 37.1 37.61 37.545 19 39.31 40.46 47.48 39.21 20 48 49 49 51.5 21 61 61 61 61 22 0.009797 0.008836 0.008388 0.039744 23 0.003773 0.002963 0.002531 0.011524 24 0.000842 0.000819 0.000729 0.0034 25 17182.54 16833.33 23055.66 20833.33 26 6581.384 5656.266 6882.516 6039.66 27 1472.184 1560.8 2005.713 1780.966 28 3.256972 3.276912 3.430244 2.773618 29 28.27737 41.3294 92.8963 218.1545 30 75.36597 83.49002 143.9019 328.9701 Table 26: Provided are the values of each of the parameters (as described in Table 23 above) measured in B. juncea 2 varieties at the indicated population densities under normal conditions. For example, “line 2-density: 200” refers to Juncea variety 2 grown at a population density of 200 plants per m².

TABLE 27 Correlation between the expression level of selected genes of some embodiments of the invention in various tissues and the phenotypic performance under normal conditions at different densities across B. Juncea accessions Corr. Gene Exp. Corr. Gene Exp. Set Name R P value set Set ID Name R P value set ID LYD347 0.81 2.84E−02 2 13 LYD347 0.73 6.45E−02 2 21 LYD348 0.71 7.58E−02 2 26 LYD351 0.84 1.78E−02 2 6 LYD351 0.76 4.93E−02 2 5 LYD351 0.80 3.02E−02 2 4 LYD352 0.89 6.74E−03 2 9 LYD352 0.90 5.09E−03 2 8 LYD352 0.91 4.34E−03 2 1 LYD352 0.88 9.54E−03 2 7 LYD352 0.91 4.60E−03 2 15 LYD352 0.76 4.95E−02 2 16 LYD352 0.95 9.24E−04 2 24 LYD352 0.91 4.48E−03 2 13 LYD352 0.95 9.57E−04 2 29 LYD352 0.83 2.19E−02 2 11 LYD352 0.96 6.22E−04 2 2 LYD352 0.82 2.37E−02 2 14 LYD352 0.95 1.11E−03 2 23 LYD352 0.95 1.16E−03 2 30 LYD352 0.84 1.90E−02 2 21 LYD352 0.96 7.54E−04 2 22 LYD354 0.94 1.36E−03 2 9 LYD354 0.91 4.65E−03 2 8 LYD354 0.98 6.32E−05 2 1 LYD354 0.93 2.58E−03 2 7 LYD354 0.80 3.11E−02 2 3 LYD354 0.88 8.26E−03 2 15 LYD354 0.88 8.18E−03 2 16 LYD354 0.96 5.17E−04 2 24 LYD354 0.84 1.69E−02 2 12 LYD354 0.91 4.10E−03 2 13 LYD354 0.96 4.81E−04 2 29 LYD354 0.76 4.55E−02 2 11 LYD354 0.97 3.23E−04 2 2 LYD354 0.99 3.80E−05 2 14 LYD354 0.96 5.20E−04 2 23 LYD354 0.96 6.03E−04 2 30 LYD354 0.92 3.42E−03 2 21 LYD354 0.96 6.14E−04 2 22 LYD355 0.89 7.35E−03 2 5 LYD357 0.76 4.65E−02 2 9 LYD357 0.78 3.83E−02 2 8 LYD357 0.76 4.88E−02 2 7 LYD357 0.76 4.52E−02 2 15 LYD357 0.75 5.22E−02 2 24 LYD357 0.75 5.38E−02 2 12 LYD357 0.77 4.35E−02 2 29 LYD357 0.83 2.20E−02 2 11 LYD357 0.75 5.01E−02 2 2 LYD357 0.74 5.71E−02 2 23 LYD357 0.77 4.48E−02 2 30 LYD357 0.76 4.68E−02 2 22 LYD358 0.79 3.44E−02 2 9 LYD358 0.79 3.65E−02 2 8 LYD358 0.72 6.57E−02 2 1 LYD358 0.78 3.87E−02 2 7 LYD358 0.75 5.36E−02 2 3 LYD358 0.75 5.09E−02 2 15 LYD358 0.87 1.05E−02 2 16 LYD358 0.93 2.62E−03 2 12 LYD358 0.88 8.16E−03 2 14 LYD360 0.85 1.57E−02 2 9 LYD360 0.93 2.36E−03 2 8 LYD360 0.78 3.78E−02 2 1 LYD360 0.81 2.62E−02 2 7 LYD360 0.94 1.87E−03 2 15 LYD360 0.96 6.16E−04 2 16 LYD360 0.87 1.10E−02 2 24 LYD360 0.97 2.30E−04 2 12 LYD360 0.79 3.33E−02 2 13 LYD360 0.86 1.29E−02 2 29 LYD360 0.95 8.96E−04 2 11 LYD360 0.87 1.01E−02 2 2 LYD360 0.84 1.75E−02 2 14 LYD360 0.86 1.24E−02 2 23 LYD360 0.88 9.10E−03 2 30 LYD360 0.89 7.66E−03 2 22 LYD361 0.75 5.01E−02 2 13 LYD361 0.79 3.38E−02 2 21 LYD362 0.78 3.75E−02 2 9 LYD362 0.75 5.21E−02 2 8 LYD362 0.86 1.28E−02 2 19 LYD362 0.84 1.70E−02 2 27 LYD362 0.74 5.47E−02 2 1 LYD362 0.72 6.89E−02 2 7 LYD362 0.76 4.69E−02 2 15 LYD362 0.76 4.92E−02 2 24 LYD362 0.77 4.33E−02 2 29 LYD362 0.82 2.53E−02 2 11 LYD362 0.76 4.58E−02 2 2 LYD362 0.71 7.65E−02 2 14 LYD362 0.76 4.79E−02 2 23 LYD362 0.77 4.16E−02 2 30 LYD362 0.76 4.95E−02 2 22 LYD362 0.80 3.24E−02 2 26 LYD364 0.74 5.61E−02 2 6 LYD364 0.75 5.13E−02 2 28 LYD364 0.75 5.25E−02 2 4 LYD365 0.72 6.78E−02 2 18 LYD366 0.91 4.39E−03 2 5 LYD497 0.75 5.27E−02 2 5 LYD498 0.83 2.09E−02 2 5 LYD499 0.76 4.79E−02 2 1 LYD499 0.78 3.69E−02 2 24 LYD499 0.85 1.42E−02 2 13 LYD499 0.78 4.03E−02 2 29 LYD499 0.77 4.33E−02 2 2 LYD499 0.79 3.55E−02 2 23 LYD499 0.73 6.11E−02 2 30 LYD499 0.96 5.73E−04 2 21 LYD499 0.76 4.68E−02 2 22 LYD499 0.92 3.61E−03 2 17 LYD501 0.71 7.41E−02 2 15 LYD501 0.85 1.56E−02 2 16 LYD501 0.82 2.45E−02 2 12 LYD501 0.76 4.65E−02 2 11 LYD501 0.74 5.64E−02 2 5 Table 27. Provided are the correlations (R) between the expression levels of yield improving genes and their homologues in tissues [meristem and flower; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.) ID] under normal conditions across B, juncea accessions. P = p value.

Example 7 Production of Sorghum Transcriptom and High Throughput Correlation Analysis with ABST Related Parameters Using 44K Sorghum Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis between plant phenotype and gene expression level, the present inventors utilized a sorghum oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. The array oligonucleotide represents about 44,000 sorghum genes and transcripts. In order to define correlations between the levels of RNA expression with ABST, yield and NUE components or vigor related parameters, various plant characteristics of 17 different sorghum hybrids were analyzed. Among them, 10 hybrids encompassing the observed variance were selected for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html].

Correlation of Sorghum Varieties Across Ecotypes Grown Under Regular Growth Conditions, Severe Drought Conditions and Low Nitrogen Conditions

Experimental Procedures

17 Sorghum varieties were grown in 3 repetitive plots, in field. Briefly, the growing protocol was as follows:

1. Regular (normal) growth conditions: sorghum plants were grown in the field using commercial fertilization and irrigation protocols (370 liter per meter², fertilization of 14 units of 21% urea per entire growth period).

2. Drought conditions: sorghum seeds were sown in soil and grown under normal condition until around 35 days from sowing, around stage V8 (eight green leaves are fully expanded, booting not started yet). At this point, irrigation was stopped, and severe drought stress was developed.

3. Low Nitrogen fertilization conditions: sorghum plants were fertilized with 50% less amount of nitrogen in the field than the amount of nitrogen applied in the regular growth treatment. All the fertilizer was applied before flowering.

Analyzed Sorghum tissues—All 10 selected Sorghum hybrids were sample per each treatment. Tissues [Flag leaf, Flower meristem and Flower] from plants growing under normal conditions, severe drought stress and low nitrogen conditions were sampled and RNA was extracted as described above. Each micro-array expression information tissue type has received a Set ID as summarized in Table 28 below.

TABLE 28 Sorghum transcriptom expression sets Expression Set Set ID Flag leaf at flowering stage under drought growth conditions 1 Flag leaf at flowering stage under low nitrogen growth conditions 2 Flag leaf at flowering stage under normal growth conditions 3 Flower meristem at flowering stage under drought growth 4 conditions Flower meristem at flowering stage under low nitrogen growth 5 conditions Flower meristem at flowering stage under normal growth 6 conditions Flower at flowering stage under drought growth conditions 7 Flower at flowering stage under low nitrogen growth conditions 8 Flower at flowering stage under normal growth conditions 9 Table 28: Provided are the sorghum transcriptom expression sets 1-9. Flag leaf = the leaf below the flower; Flower meristem = Apical meristem following panicle initiation; Flower = the flower at the anthesis day. Expression sets 1, 4 and 7 are from plants grown under drought conditions; Expresion sets 2, 5 and 8 are from plants grown under low nitrogen conditions; Expression sets 3, 6 and 9 are from plants grown under normal conditions.

The following parameters were collected using digital imaging system: At the end of the growing period the grains were separated from the Plant ‘Head’ and the following parameters were measured and collected:

Average Grain Area (cm²)—A sample of ˜200 grains were weight, photographed and images were processed using the below described image processing system. The grain area was measured from those images and was divided by the number of grains.

(I) Upper and Lower Ratio Average of Grain Area, width, diameter and perimeter—Grain projection of area, width, diameter and perimeter were extracted from the digital images using open source package imagej (nih). Seed data was analyzed in plot average levels as follows:

Average of all seeds.

Average of upper 20% fraction—contained upper 20% fraction of seeds.

Average of lower 20% fraction—contained lower 20% fraction of seeds.

Further on, ratio between each fraction and the plot average was calculated for each of the data parameters.

At the end of the growing period 5 ‘Heads’ were, photographed and images were processed using the below described image processing system.

(II) Head Average Area (cm²)—At the end of the growing period 5 ‘Heads’ were, photographed and images were processed using the below described image processing system. The ‘Head’ area was measured from those images and was divided by the number of ‘Heads’.

(III) Head Average Length (cm)—At the end of the growing period 5 ‘Heads’ were, photographed and images were processed using the below described image processing system. The ‘Head’ length (longest axis) was measured from those images and was divided by the number of ‘Heads’.

(IV) Head Average width (cm)—At the end of the growing period 5 ‘Heads’ were, photographed and images were processed using the below described image processing system. The ‘Head’ width was measured from those images and was divided by the number of ‘Heads’.

(V) Head Average width (cm)—At the end of the growing period 5 ‘Heads’ were, photographed and images were processed using the below described image processing system. The ‘Head’ perimeter was measured from those images and was divided by the number of ‘Heads’.

The image processing system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.37, Java based image processing software, which was developed at the U.S. National Institutes of Health and is freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/. Images were captured in resolution of 10 Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, image processing output data for seed area and seed length was saved to text files and analyzed using the JMP statistical analysis software (SAS institute).

Additional parameters were collected either by sampling 5 plants per plot or by measuring the parameter across all the plants within the plot.

Total Grain Weight/Head (gr.) (grain yield)—At the end of the experiment (plant ‘Heads’) heads from plots within blocks A-C were collected. 5 heads were separately threshed and grains were weighted, all additional heads were threshed together and weighted as well. The average grain weight per head was calculated by dividing the total grain weight by number of total heads per plot (based on plot). In case of 5 heads, the total grains weight of 5 heads was divided by 5.

FW Head/Plant gram—At the end of the experiment (when heads were harvested) total and 5 selected heads per plots within blocks A-C were collected separately. The heads (total and 5) were weighted (gr.) separately and the average fresh weight per plant was calculated for total (FW Head/Plant gr. based on plot) and for 5 (FW Head/Plant gr. based on 5 plants).

Plant height—Plants were characterized for height during growing period at 5 time points. In each measure, plants were measured for their height using a measuring tape. Height was measured from ground level to top of the longest leaf.

SPAD—Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed 64 days post sowing. SPAD meter readings were done on young fully developed leaf. Three measurements per leaf were taken per plot.

Vegetative fresh weight and Heads—At the end of the experiment (when Inflorescence were dry) all Inflorescence and vegetative material from plots within blocks A-C were collected. The biomass and Heads weight of each plot was separated, measured and divided by the number of Heads.

Plant biomass (Fresh weight)—At the end of the experiment (when Inflorescence were dry) the vegetative material from plots within blocks A-C were collected. The plants biomass without the Inflorescence were measured and divided by the number of Plants.

FW Heads/(FW Heads+FW Plants)—The total fresh weight of heads and their respective plant biomass were measured at the harvest day. The heads weight was divided by the sum of weights of heads and plants.

Experimental Results

17 different sorghum varieties were grown and characterized for different parameters (Table 29). The average for each of the measured parameter was calculated using the JMP software (Tables 30-31) and a subsequent correlation analysis between the various transcriptom sets (Table 28) and the average parameters (Tables 30-31) was conducted Results were then integrated to the database (Table 32).

TABLE 29 Sorghum correlated parameters (vectors) Correlation Correlated parameter with ID Total grain weight/Head gr (based on plot), Normal 1 Total grain weight/Head gr (based on 5 heads), Normal 2 Head Average Area (cm²), Normal 3 Head Average Perimeter (cm), Normal 4 Head Average Length (cm), Normal 5 Head Average Width (cm), Normal 6 Average Grain Area (cm²), Normal 7 Upper Ratio Average Grain Area, Normal 8 Lower Ratio Average Grain Area, Normal 9 Lower Ratio Average Grain Perimeter, Normal 10 Lower Ratio Average Grain Length, Normal 11 Lower Ratio Average Grain Width, Normal 12 Final Plant Height (cm), Normal 13 FW - Head/Plant gr (based on 5 plants), Normal 14 FW - Head/Plant gr (based on plot), Normal 15 FW/Plant gr (based on plot), Normal 16 Leaf SPAD 64 DPS (Days Post Sowing), Normal 17 FW Heads/(FW Heads + FW Plants)(all plot), Normal 18 [Plant biomass (FW)/SPAD 64 DPS], Normal 19 [Grain Yield + plant biomass/SPAD 64 DPS], Normal 20 [Grain yield/SPAD 64 DPS], Normal 21 Total grain weight/Head (based on plot) gr., Low N 22 Total grain weight/Head gr (based on 5 heads), Low N 23 Head Average Area (cm²), Low N 24 Head Average Perimeter (cm), Low N 25 Head Average Length (cm), Low N 26 Head Average Width (cm), Low N 27 Average Grain Area (cm²), Low N 28 Upper Ratio Average Grain Area, Low N 29 Lower Ratio Average Grain Area, Low N 30 Lower Ratio Average Grain Perimeter, Low N 31 Lower Ratio Average Grain Length, Low N 32 Lower Ratio Average Grain Width, Low N 33 Final Plant Height (cm), Low N 34 FW - Head/Plant gr. (based on 5 plants), Low N 35 FW - Head/Plant gr. (based on plot), Low N 36 FW/Plant gr. (based on plot), Low N 37 Leaf SPAD 64 DPS (Days Post Sowing), Low N 38 FW Heads/(FW Heads + FW Plants)(all plot), Low N 39 [Plant biomass (FW)/SPAD 64 DPS], Low N 40 [Grain Yield + plant biomass/SPAD 64 DPS], Low N 41 [Grain yield/SPAD 64 DPS], Low N 42 Total grain weight/Head gr, (based on plot) Drought 43 Head Average Area (cm²), Drought 44 Head Average Perimeter (cm), Drought 45 Head Average Length (cm), Drought 46 Head Average Width (cm), Drought 47 Average Grain Area (cm²), Drought 48 Upper Ratio Average Grain Area, Drought 49 Final Plant Height (cm), Drought 50 FW - Head/Plant gr. (based on plot), Drought 51 FW/Plant gr (based on plot), Drought 52 Leaf SPAD 64 DPS (Days Post Sowing), Drought 53 FW Heads/(FW Heads + FW Plants)(all plot), Drought 54 [Plant biomass (FW)/SPAD 64 DPS], Drought 55 Table 29. Provided are the Sorghum correlated parameters (vectors). “gr.” = grams; “SPAD” = chlorophyll levels; “FW” = Plant Fresh weight; “normal” = standard growth conditions.

TABLE 30 Measured parameters in Sorghum accessions (Lines 1-9) Ecotype/ Correlation ID No. Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 Line-8 Line-9 1 31.12 26.35 18.72 38.38 26.67 28.84 47.67 31.00 39.99 2 47.40 46.30 28.37 70.40 32.15 49.23 63.45 44.45 56.65 3 120.14 167.60 85.14 157.26 104.00 102.48 168.54 109.32 135.13 4 61.22 67.90 56.26 65.38 67.46 67.46 74.35 56.16 61.64 5 25.58 26.84 21.02 26.84 23.14 21.82 31.33 23.18 25.70 6 5.97 7.92 4.87 7.43 5.58 5.88 6.78 5.99 6.62 7 0.10 0.11 0.13 0.13 0.14 0.14 0.11 0.11 0.10 8 1.22 1.30 1.13 1.14 1.16 1.15 1.19 1.23 1.25 9 0.83 0.74 0.78 0.80 0.70 0.70 0.83 0.81 0.84 10 0.91 0.87 0.91 0.95 0.90 0.91 0.91 0.91 0.92 11 0.91 0.88 0.92 0.91 0.89 0.88 0.91 0.90 0.92 12 0.91 0.83 0.85 0.87 0.79 0.80 0.90 0.89 0.91 13 95.25 79.20 197.85 234.20 189.40 194.67 117.25 92.80 112.65 14 406.50 518.00 148.00 423.00 92.00 101.33 423.50 386.50 409.50 15 175.15 223.49 56.40 111.62 67.34 66.90 126.18 107.74 123.86 16 162.56 212.59 334.83 313.46 462.28 318.26 151.13 137.60 167.98 17 43.01 . 43.26 44.74 45.76 41.61 45.21 45.14 43.03 18 0.51 0.51 0.12 0.26 0.12 0.18 0.46 0.43 0.42 19 0.72 0.43 0.86 0.58 0.69 1.05 0.69 0.93 0.84 20 4.50 8.17 7.87 10.68 8.34 4.40 3.74 4.83 3.67 21 3.78 7.74 7.01 10.10 7.65 3.34 3.05 3.90 2.83 22 25.95 30.57 19.37 35.62 25.18 22.18 49.96 27.48 51.12 23 50.27 50.93 36.13 73.10 37.87 36.40 71.67 35.00 76.73 24 96.24 214.72 98.59 182.83 119.64 110.19 172.36 84.81 156.25 25 56.32 79.20 53.25 76.21 67.27 59.49 79.28 51.52 69.88 26 23.22 25.58 20.93 28.43 24.32 22.63 32.11 20.38 26.69 27 5.26 10.41 5.93 8.25 6.19 6.12 6.80 5.25 7.52 28 0.11 0.11 0.14 0.12 0.14 0.13 0.12 0.12 0.12 29 1.18 1.31 1.11 1.21 1.19 1.18 1.16 1.23 1.17 30 0.82 0.77 0.81 0.79 0.78 0.80 0.83 0.79 0.81 31 0.90 0.88 0.92 0.90 0.92 0.92 0.92 0.89 0.90 32 0.91 0.90 0.92 0.90 0.91 0.93 0.92 0.89 0.90 33 0.90 0.85 0.89 0.88 0.86 0.87 0.91 0.89 0.90 34 104.00 80.93 204.73 125.40 225.40 208.07 121.40 100.27 121.13 35 388.00 428.67 297.67 280.00 208.33 303.67 436.00 376.33 474.67 36 214.78 205.05 73.49 122.96 153.07 93.23 134.11 77.43 129.63 37 204.78 199.64 340.51 240.60 537.78 359.40 149.20 129.06 178.71 38 38.33 38.98 42.33 40.90 43.15 39.85 42.68 43.31 39.01 39 0.51 0.51 0.17 0.39 0.21 0.19 0.48 0.37 0.42 40 5.34 5.12 8.05 5.88 12.46 9.02 3.50 2.98 4.58 41 6.02 5.91 8.50 6.75 13.05 9.58 4.67 3.61 5.89 42 0.68 0.78 0.46 0.87 0.58 0.56 1.17 0.63 1.31 43 22.11 16.77 9.19 104.44 3.24 22.00 9.97 18.58 29.27 44 83.14 107.79 88.68 135.91 90.76 123.95 86.06 85.20 113.10 45 52.78 64.49 56.59 64.37 53.21 71.66 55.61 52.96 69.83 46 21.63 21.94 21.57 22.01 20.99 28.60 21.35 20.81 24.68 47 4.83 6.31 5.16 7.78 5.28 5.49 5.04 5.07 5.77 48 0.10 0.11 0.11 0.09 0.09 0.11 49 1.31 1.19 1.29 1.46 1.21 1.21 50 89.40 75.73 92.10 94.30 150.80 110.73 99.20 84.00 99.00 51 154.90 122.02 130.51 241.11 69.03 186.41 62.11 39.02 58.94 52 207.99 138.02 255.41 402.22 233.55 391.75 89.31 50.61 87.02 53 40.58 40.88 45.01 42.30 45.24 40.56 44.80 45.07 40.65 54 0.42 0.47 0.42 0.37 0.23 0.31 0.41 0.44 0.40 55 5.13 3.38 5.67 9.51 5.16 9.66 1.99 1.12 2.14 Table 30: Provided are the values of each of the parameters (as described in Table 29 above) measured in Sorghum accessions (ecotype) under normal, low nitrogen and drought conditions. Growth conditions are specified in the experimental procedure section.

TABLE 31 Additional measured parameters in Sorghum accessions (Lines 10-17) Ecotype/Correlation Line- Line- Line- Line- Line- ID No. 10 Line-11 Line-12 13 14 15 16 Line-17 1 38.36 32.10 32.69 32.79 51.53 35.71 38.31 42.44 2 60.00 45.45 58.19 70.60 70.10 53.95 59.87 52.65 3 169.03 156.10 112.14 154.74 171.70 168.51 162.51 170.46 4 71.40 68.56 56.44 67.79 71.54 78.94 67.03 74.11 5 28.82 28.13 22.97 28.09 30.00 30.54 27.17 29.26 6 7.42 6.98 6.19 7.02 7.18 7.00 7.39 7.35 7 0.12 0.12 0.11 0.12 0.11 0.10 0.11 0.11 8 1.24 1.32 1.22 1.18 1.18 1.22 1.25 1.22 9 0.79 0.77 0.80 0.81 0.82 0.81 0.82 0.82 10 0.93 0.91 0.92 0.90 0.91 0.90 0.91 0.91 11 0.92 0.89 0.91 0.91 0.91 0.90 0.90 0.91 12 0.85 0.86 0.88 0.90 0.90 0.91 0.90 0.90 13 97.50 98.00 100.00 105.60 151.15 117.10 124.45 126.50 14 328.95 391.00 435.75 429.50 441.00 415.75 429.50 428.50 15 102.75 82.33 77.59 91.17 150.44 109.10 107.58 130.88 16 128.97 97.62 99.32 112.24 157.42 130.55 135.66 209.21 17 45.59 44.83 45.33 46.54 43.99 45.09 45.14 43.13 18 0.44 0.46 0.45 0.45 0.51 0.46 0.44 0.39 19 0.72 0.72 0.70 1.17 0.79 0.85 0.98 20 2.89 2.91 3.12 4.75 3.69 3.85 5.84 21 2.18 2.19 2.41 3.58 2.90 3.01 4.85 22 36.84 29.45 26.70 29.42 51.12 37.04 39.85 41.78 23 57.58 42.93 36.47 68.60 71.80 49.27 43.87 52.07 24 136.71 137.70 96.54 158.19 163.95 138.39 135.46 165.64 25 66.17 67.37 57.90 70.61 73.76 66.87 65.40 75.97 26 26.31 25.43 23.11 27.87 28.88 27.64 25.52 30.33 27 6.59 6.85 5.32 7.25 7.19 6.27 6.57 6.82 28 0.13 0.13 0.12 0.12 0.11 0.11 0.12 0.11 29 1.22 1.24 1.19 1.23 1.16 1.34 1.21 1.21 30 0.77 0.74 0.80 0.79 0.82 0.80 0.81 0.81 31 0.91 0.89 0.90 0.90 0.91 0.89 0.90 0.90 32 0.91 0.89 0.90 0.89 0.91 0.89 0.89 0.90 33 0.86 0.84 0.90 0.89 0.91 0.90 0.90 0.90 34 94.53 110.00 115.07 104.73 173.67 115.60 138.80 144.40 35 437.67 383.00 375.00 425.00 434.00 408.67 378.50 432.00 36 99.83 76.95 84.25 92.24 138.83 113.32 95.50 129.49 37 124.27 101.33 132.12 117.90 176.99 143.67 126.98 180.45 38 42.71 40.08 43.98 45.44 44.75 42.58 43.81 46.73 39 0.44 0.43 0.39 0.44 0.44 0.44 0.43 0.42 40 2.91 2.53 3.00 2.60 3.96 3.38 2.90 3.86 41 3.77 3.26 3.61 3.24 5.10 4.25 3.81 4.76 42 0.86 0.73 0.61 0.65 1.14 0.87 0.91 0.89 43 10.45 14.77 12.86 18.24 11.60 18.65 16.36 44 100.79 80.41 126.89 86.41 92.29 77.89 76.93 45 65.14 55.27 69.06 53.32 56.29 49.12 51.88 46 24.28 21.95 24.98 19.49 20.42 16.81 18.88 47 5.37 4.66 6.35 5.58 5.76 5.86 5.10 50 92.20 81.93 98.80 86.47 99.60 83.00 83.53 92.30 51 76.37 33.47 42.20 41.53 131.67 60.84 44.33 185.44 52 120.43 37.21 48.18 44.20 231.60 116.01 123.08 342.50 53 45.43 42.58 44.18 44.60 42.41 43.25 40.30 40.75 54 0.44 0.47 0.47 0.48 0.35 0.35 0.23 0.33 55 2.65 0.87 1.09 0.99 5.46 2.68 3.05 8.40 Table 31: Provided are the values of each of the parameters (as described above) measured in Sorghum accessions (ecotype) under normal, low nitrogen and drought conditions. Growth conditions are specified in the experimental procedure section.

TABLE 32 Correlation between the expression level of selected genes of some embodiments of the invention in various tissues and the phenotypic performance under normal or abiotic stress conditions across Sorghum accessions Corr. Corr. Gene Exp. Set Gene Exp. Set Name R P value set ID Name R P value set ID LYD423 0.77 8.63E−03 6 13 LYD423 0.72 1.85E−02 6 15 LYD423 0.80 5.31E−03 6 16 LYD423 0.81 4.12E−03 6 1 LYD423 0.94 6.58E−05 2 29 LYD423 0.84 2.13E−03 4 55 LYD423 0.70 2.37E−02 4 51 LYD423 0.84 2.18E−03 4 52 LYD423 0.91 2.94E−04 5 36 LYD423 0.73 1.72E−02 5 30 LYD423 0.86 1.23E−03 5 41 LYD423 0.91 2.82E−04 5 40 LYD423 0.71 2.20E−02 5 39 LYD423 0.85 2.08E−03 5 32 LYD423 0.89 5.04E−04 5 37 LYD423 0.76 1.15E−02 3 7 LYD423 0.72 2.95E−02 7 44 LYD423 0.76 1.81E−02 7 47 LYD424 0.86 1.41E−03 6 13 LYD424 0.72 1.87E−02 6 1 LYD424 0.83 2.76E−03 4 55 LYD424 0.80 5.92E−03 4 51 LYD424 0.84 2.20E−03 4 52 LYD425 0.82 3.55E−03 6 13 LYD425 0.84 2.37E−03 6 1 LYD425 0.73 1.58E−02 5 35 LYD425 0.71 2.25E−02 5 22 LYD425 0.85 1.74E−03 1 55 LYD425 0.72 1.95E−02 1 51 LYD425 0.86 1.32E−03 1 52 LYD427 0.77 9.39E−03 6 13 LYD427 0.87 1.03E−03 6 1 LYD427 0.73 1.75E−02 6 2 LYD427 0.71 2.11E−02 6 11 LYD427 0.89 4.79E−04 9 2 LYD427 0.82 4.05E−03 4 55 LYD427 0.72 1.87E−02 4 51 LYD427 0.82 3.41E−03 4 52 LYD427 0.71 2.16E−02 5 30 LYD427 0.73 1.58E−02 5 37 LYD427 0.81 4.42E−03 3 2 LYD427 0.71 2.05E−02 1 50 LYD428 0.73 1.59E−02 2 34 LYD431 0.74 1.42E−02 6 13 LYD431 0.87 9.18E−04 4 55 LYD431 0.72 1.85E−02 4 51 LYD431 0.86 1.24E−03 4 52 LYD432 0.71 2.07E−02 6 8 LYD432 0.70 2.31E−02 6 7 LYD432 0.79 6.56E−03 2 34 LYD432 0.83 3.06E−03 8 28 LYD432 0.72 1.85E−02 3 2 LYD432 0.73 1.69E−02 1 53 LYD433 0.73 1.60E−02 6 5 LYD433 0.81 4.12E−03 6 2 LYD433 0.70 3.45E−02 4 44 LYD433 0.70 2.39E−02 5 30 LYD434 0.73 1.56E−02 6 13 LYD434 0.74 1.35E−02 4 55 LYD434 0.79 6.92E−03 4 51 LYD434 0.75 1.29E−02 4 52 LYD434 0.91 7.59E−04 7 44 LYD434 0.81 7.61E−03 7 47 LYD434 0.91 6.53E−04 7 45 LYD434 0.72 2.77E−02 7 46 LYD435 0.76 9.94E−03 6 7 LYD435 0.72 1.97E−02 9 1 LYD436 0.85 1.95E−03 6 13 LYD436 0.77 9.58E−03 6 1 LYD436 0.92 1.39E−04 4 55 LYD436 0.84 2.39E−03 4 51 LYD436 0.93 1.13E−04 4 52 LYD436 0.77 9.25E−03 8 28 LYD436 0.75 1.17E−02 5 37 LYD507 0.71 2.17E−02 9 1 LYD507 0.77 8.97E−03 8 32 LYD507 0.74 1.54E−02 8 31 LYD508 0.76 1.03E−02 6 1 LYD508 0.75 1.16E−02 4 55 LYD508 0.77 9.61E−03 4 52 LYD508 0.77 8.64E−03 5 22 LYD508 0.71 2.11E−02 5 42 LYD508 0.73 1.72E−02 3 16 LYD509 0.81 4.73E−03 6 8 LYD509 0.71 2.16E−02 9 13 LYD509 0.80 4.97E−03 9 1 LYD509 0.74 2.22E−02 7 44 LYD509 0.78 1.38E−02 7 47 LYD509 0.71 3.30E−02 1 44 LYD509 0.70 3.41E−02 1 45 LYD509 0.81 7.56E−03 1 46 LYD510 0.79 6.74E−03 6 13 LYD510 0.73 1.76E−02 6 18 LYD510 0.71 2.21E−02 6 4 LYD510 0.73 1.68E−02 6 5 LYD510 0.75 1.17E−02 6 1 LYD510 0.87 1.03E−03 4 55 LYD510 0.75 1.33E−02 4 51 LYD510 0.87 9.50E−04 4 52 LYD510 0.75 1.32E−02 5 37 Table 32. Provided are the correlations (R) between the expression levels of yield improving genes and their homologues in tissues [Flag leaf, Flower meristem, stem and Flower; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.) ID] under stress conditions or normal conditions across Sorghum accessions. P = p value.

Example 8 Production of Maize Transcriptom and High Throughput Correlation Analysis with Yield and NUE Related Parameters Using 60K Maize Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis between plant phenotype and gene expression level, the present inventors utilized a maize oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. The array oligonucleotide represents about 60,000 maize genes and transcripts.

Correlation of Maize Hybrids Across Ecotypes Grown Under Regular Growth Conditions

Experimental Procedures

12 Maize hybrids were grown in 3 repetitive plots, in field. Maize seeds were planted and plants were grown in the field using commercial fertilization and irrigation protocols. In order to define correlations between the levels of RNA expression with stress and yield components or vigor related parameters, the 12 different maize hybrids were analyzed. Among them, 10 hybrids encompassing the observed variance were selected for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html].

Analyzed Maize tissues—All 10 selected maize hybrids were sampled per 3 time points (TP2=V6-V8, TP5=R1-R2, TP6=R3-R4). Four types of plant tissues [Ear, flag leaf indicated in Table 33 as “leaf”, grain distal part, and internode] growing under Normal conditions were sampled and RNA was extracted as described above. Each micro-array expression information tissue type has received a Set ID as summarized in Table 33 below.

TABLE 33 Maize transcriptom expression sets under normal conditions Set Expression Set ID Ear at reproductive stage (R1-R2) 1 Leaf at reproductive stage (R3-R4) 2 Leaf at vegetative stage (V2-V3) 3 Internode at vegetative stage (V2-V3) 4 Internode at reproductive stage (R3-R4) 5 Ear at reproductive stage (R3-R4) 6 Internode at reproductive stage (R1-R2) 7 Leaf at reproductive stage (R1-R2) 8 Table 33: Provided are the identification (ID) number of each of the Maize expression sets. Leaf = the leaf below the main ear; Ear = the female flower at the anthesis day; Internodes = internodes located above and below the main ear in the plant.

The following parameters were collected using digital imaging system:

Grain Area (cm²)—At the end of the growing period the grains were separated from the ear. A sample of ˜200 grains were weighted, photographed and images were processed using the below described image processing system. The grain area was measured from those images and was divided by the number (Num) of grains.

Grain Length and Grain width (cm)—At the end of the growing period the grains were separated from the ear. A sample of ˜200 grains were weighted, photographed and images were processed using the below described image processing system. The sum of grain lengths/or width (longest axis) was measured from those images and was divided by the number of grains.

Ear Area (cm²)—At the end of the growing period 5 ears were, photographed and images were processed using the below described image processing system. The Ear area was measured from those images and was divided by the number of Ears.

Ear Length and Ear Width (cm)—At the end of the growing period 5 ears were, photographed and images were processed using the below described image processing system. The Ear length and width (longest axis) was measured from those images and was divided by the number of ears.

The image processing system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.37, Java based image processing software, which was developed at the U.S. National Institutes of Health and is freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/. Images were captured in resolution of 10 Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, image processing output data for seed area and seed length was saved to text files and analyzed using the JMP statistical analysis software (SAS institute).

Additional parameters were collected either by sampling 6 plants per plot or by measuring the parameter across all the plants within the plot.

Normalized Grain Weight per plant (gr.)—At the end of the experiment all ears from plots within blocks A-C were collected. Six ears were separately threshed and grains were weighted, all additional ears were threshed together and weighted as well. The average grain weight per ear was calculated by dividing the total grain weight by number of total ears per plot (based on plot). In case of 6 ears, the total grains weight of 6 ears was divided by 6.

Ear FW (gr.)—At the end of the experiment (when ears were harvested) total and 6 selected ears per plots within blocks A-C were collected separately. The plants with (total and 6) were weighted (gr.) separately and the average ear per plant was calculated for total (Ear FW per plot) and for 6 (Ear FW per plant).

Plant height and Ear height—Plants were characterized for height at harvesting. In each measure, 6 plants were measured for their height using a measuring tape. Height was measured from ground level to top of the plant below the tassel. Ear height was measured from the ground level to the place were the main ear is located.

Leaf number per plant—Plants were characterized for leaf number during growing period at 5 time points. In each measure, plants were measured for their leaf number by counting all the leaves of 3 selected plants per plot.

Relative Growth Rate of leaf number—was calculated using Formula IX (above).

SPAD—Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed 64 days post sowing. SPAD meter readings were done on young fully developed leaf. Three measurements per leaf were taken per plot. Data were taken after 46 and 54 days after sowing (DPS).

Dry weight per plant—At the end of the experiment (when inflorescence were dry) all vegetative material from plots within blocks A-C were collected.

Dry weight=total weight of the vegetative portion above ground (excluding roots) after drying at 70° C. in oven for 48 hours.

Harvest Index (HI) (Maize)—The harvest index was calculated using Formula X.

Harvest Index=Average grain dry weight per Ear/(Average vegetative dry weight per Ear+Average Ear dry weight).  Formula X

Percent Filled Ear [%]—it was calculated as the percentage of the Ear area with grains out of the total ear.

Filled per Whole Ear—it was calculated as the length of the ear with grains out of the total ear.

Cob diameter [cm]—The diameter of the cob without grains was measured using a ruler.

Kernel Row Number per Ear—The number of rows in each ear was counted.

Experimental Results

12 different maize hybrids were grown and characterized for different parameters. The correlated parameters are described in Table 34 below. The average for each of the measured parameter was calculated using the JMP software (Tables 35-36) and a subsequent correlation analysis was performed (Table 37). Results were then integrated to the database.

TABLE 34 Maize correlated parameters (vectors) Correlation Correlated parameter with ID Growth Rate Leaf Num (ratio) 1 Plant Height per Plot (cm) 2 Ear Height (cm) 3 Leaf Number per Plant (number) 4 Ear Length (cm) 5 Percent Filled Ear (percent) 6 Cob Diameter (mm) 7 Kernel Row Number per Ear (number) 8 DW per Plant based on 6 (gr). 9 Ear FW per Plant based on 6 (gr). 10 Normalized Grain Weight per plant based on 6 (gr). 11 Ears FW per plant based on all (gr). 12 Normalized Grain Weight per Plant based on all (gr). 13 Ear Area (cm²) 14 Ear Width (cm) 15 Filled per Whole Ear (percent) 16 Grain Area (cm²) 17 Grain Length (cm) 18 Grain Width (cm) 19 SPAD 46DPS TP2 20 SPAD 54DPS TP5 21 Table 34. SPAD 46DPS and SPAD 54DPS: Chlorophyl level after 46 and 54 days after sowing (DPS). “FW” = fresh weight; “DW” = dry weight.

TABLE 35 Measured parameters in Maize accessions under normal conditions (lines 1-6) Ecotype/ Correlation ID No. Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 1 0.283 0.221 0.281 0.269 0.306 0.244 2 278.083 260.500 275.133 238.500 286.944 224.833 3 135.167 122.333 131.967 114.000 135.278 94.278 4 12.000 11.110 11.689 11.778 11.944 12.333 5 19.691 19.055 20.521 21.344 20.920 18.232 6 80.624 86.760 82.144 92.708 80.377 82.757 7 28.957 25.078 28.052 25.732 28.715 25.783 8 16.167 14.667 16.200 15.889 16.167 15.167 9 657.500 491.667 641.111 580.556 655.556 569.444 10 245.833 208.333 262.222 263.889 272.222 177.778 11 140.683 139.536 153.667 176.983 156.614 119.667 12 278.194 217.502 288.280 247.879 280.106 175.841 13 153.900 135.882 152.500 159.156 140.463 117.135 14 85.058 85.843 90.507 95.953 91.624 72.408 15 5.584 5.151 5.671 5.533 5.728 5.227 16 0.916 0.922 0.927 0.917 0.908 0.950 17 0.753 0.708 0.755 0.766 0.806 0.713 18 1.167 1.092 1.180 1.205 1.228 1.123 19 0.810 0.814 0.803 0.803 0.824 0.803 20 51.667 56.406 53.547 55.211 55.300 59.350 21 54.283 57.178 56.011 59.682 54.767 59.144 Table 35. Provided are the values of each of the parameters (as described above) measured in maize accessions (Seed ID) under regular growth conditions. Growth conditions are specified in the experimental procedure section.

TABLE 36 Additional measured parameters in Maize accessions under regular growth conditions (lines 7-12) Ecotype/ Correlation ID No. Line-7 Line-8 Line-9 Line-10 Line-11 Line-12 1 0.244 0.266 0.194 0.301 2 264.444 251.611 163.778 278.444 3 120.944 107.722 60.444 112.500 4 12.444 12.222 9.278 12.556 5 19.017 18.572 16.689 21.702 6 73.248 81.061 81.056 91.601 7 26.432 25.192 26.668 8 16.000 14.833 14.267 15.389 9 511.111 544.444 574.167 522.222 10 188.889 197.222 141.111 261.111 11 119.692 133.508 54.316 173.231 12 192.474 204.700 142.716 264.236 13 123.237 131.266 40.844 170.662 14 74.032 76.534 55.201 95.360 15 5.221 5.328 4.120 5.577 16 0.873 0.939 0.796 0.958 17 0.714 0.753 0.502 0.762 18 1.139 1.134 0.921 1.180 19 0.791 0.837 0.675 0.812 20 58.483 55.876 53.856 59.747 52.983 49.994 21 57.994 60.356 51.394 61.139 54.767 53.344 Table 36. Provided are the values of each of the parameters (as described above) measured in maize accessions (Seed ID) under regular growth conditions. Growth conditions are specified in the experimental procedure section.

TABLE 37 Correlation between the expression level of selected LYD genes of some embodiments of the invention in various tissues and the phenotypic performance under normal across maize accessions Corr. Corr. Gene Exp. Set Gene Exp. Set Name R P value set ID Name R P value set ID LYD391 0.75 3.14E−02 5 19 LYD391 0.82 2.28E−02 7 14 LYD391 0.75 5.23E−02 7 13 LYD391 0.81 2.86E−02 7 2 LYD391 0.92 3.41E−03 7 3 LYD391 0.82 2.50E−02 7 12 LYD391 0.77 4.39E−02 7 10 LYD391 0.74 5.55E−02 7 11 LYD391 0.93 6.47E−03 1 7 LYD391 0.80 5.59E−02 6 19 LYD503 0.81 2.75E−02 7 4 LYD503 0.81 2.88E−02 7 16 LYD503 0.76 4.79E−02 7 2 LYD503 0.86 1.26E−02 7 19 LYD503 0.89 6.73E−03 8 4 LYD503 0.88 9.13E−03 8 21 LYD503 0.71 7.16E−02 8 18 LYD503 0.85 1.61E−02 8 16 LYD503 0.72 6.56E−02 8 17 LYD503 0.71 7.11E−02 8 19 LYD503 0.75 5.03E−02 1 14 LYD503 0.71 7.51E−02 1 13 LYD503 0.79 3.45E−02 1 2 LYD503 0.88 9.31E−03 1 3 LYD503 0.70 7.77E−02 1 15 LYD503 0.82 2.43E−02 1 12 LYD503 0.73 6.20E−02 1 10 LYD503 0.91 1.30E−02 6 4 Table 37. “Corr. ID” - correlation set ID according to the correlated parameters Table 34 above. “Exp. Set”—Expression set. “R” = Pearson correlation coefficient; “P” = p value.

Example 9 Production of Soybean (Glycine Max) Transcriptom and High Throughput Correlation Analysis with Yield Parameters Using 44K B. Soybean Oligonucleotide Micro-Arrays

In order to produce a high throughput correlation analysis, the present inventors utilized a Soybean oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. The array oligonucleotide represents about 42,000 Soybean genes and transcripts. In order to define correlations between the levels of RNA expression with yield components or plant architecture related parameters or plant vigor related parameters, various plant characteristics of 29 different Glycine max varieties were analyzed and 12 varieties were further used for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test.

Correlation of Glycine max Genes' Expression Levels with Phenotypic Characteristics Across Ecotype

Experimental Procedures

29 Soybean varieties were grown in three repetitive plots, in field. Briefly, the growing protocol was as follows: Soybean seeds were sown in soil and grown under normal conditions until harvest. In order to define correlations between the levels of RNA expression with yield components or plant architecture related parameters or vigor related parameters, 12 different Soybean varieties (out of 29 varieties) were analyzed and used for gene expression analyses. Analysis was performed at two pre-determined time periods: at pod set (when the soybean pods are formed) and at harvest time (when the soybean pods are ready for harvest, with mature seeds). Table 39 describes the soybean correlated parameters. The average for each of the measured parameter was calculated using the JMP software (Tables 40-41) and a subsequent correlation analysis was performed (Table 42). Results were then integrated to the database.

TABLE 38 Soybean transcriptom expression sets Expression Set Set ID Apical meristem at vegetative stage under normal growth 1 condition Leaf at vegetative stage under normal growth condition 2 Leaf at flowering stage under normal growth condition 3 Leaf at pod setting stage under normal growth condition 4 Root at vegetative stage under normal growth condition 5 Root at flowering stage under normal growth condition 6 Root at pod setting stage under normal growth condition 7 Stem at vegetative stage under normal growth condition 8 Stem at pod setting stage under normal growth condition 9 Flower bud at flowering stage under normal growth condition 10 Pod (R3-R4) at pod setting stage under normal growth condition 11 Table 38: Provided are the soybean transcriptom expression sets.

RNA extraction—All 12 selected Soybean varieties were sample per treatment. Plant tissues [leaf, root. Stem. Pod, apical meristem. Flower buds] growing under normal conditions were sampled and RNA was extracted as described above.

The collected data parameters were as follows:

Main branch base diameter [mm] at pod set—the diameter of the base of the main branch (based diameter) average of three plants per plot.

Fresh weight [gr/plant] at pod set—total weight of the vegetative portion above ground (excluding roots) before drying at pod set, average of three plants per plot.

Dry weight [gr/plant] at pod set—total weight of the vegetative portion above ground (excluding roots) after drying at 70° C. in oven for 48 hours at pod set, average of three plants per plot.

Total number of nodes with pods on lateral branches [value/plant]—counting of nodes which contain pods in lateral branches at pod set, average of three plants per plot.

Number of lateral branches at pod set [value/plant]—counting number of lateral branches at pod set, average of three plants per plot.

Total weight of lateral branches at pod set [gr/plant]—weight all lateral branches at pod set, average of three plants per plot.

Total weight of pods on main stem at pod set [gr/plant]—weight all pods on main stem at pod set, average of three plants per plot.

Total number of nodes on main stem [value/plant]—count of number of nodes on main stem starting from first node above ground, average of three plants per plot.

Total number of pods with 1 seed on lateral branches at pod set [value/plant]-count the number of pods containing 1 seed in all lateral branches at pod set, average of three plants per plot.

Total number of pods with 2 seeds on lateral branches at pod set [value/plant]—count the number of pods containing 2 seeds in all lateral branches at pod set, average of three plants per plot.

Total number of pods with 3 seeds on lateral branches at pod set [value/plant]—count the number of pods containing 3 seeds in all lateral branches at pod set, average of three plants per plot.

Total number of pods with 4 seeds on lateral branches at pod set [value/plant]—count the number of pods containing 4 seeds in all lateral branches at pod set, average of three plants per plot.

Total number of pods with 1 seed on main stem at pod set [value/plant]—count the number of pods containing 1 seed in main stem at pod set, average of three plants per plot.

Total number of pods with 2 seeds on main stem at pod set [value/plant]-count the number of pods containing 2 seeds in main stem at pod set, average of three plants per plot.

Total number of pods with 3 seeds on main stem at pod set [value/plant]-count the number of pods containing 3 seeds in main stem at pod set, average of three plants per plot.

Total number of pods with 4 seeds on main stem at pod set [value/plant]-count the number of pods containing 4 seeds in main stem at pod set, average of three plants per plot.

Total number of seeds per plant at pod set [value/plant]—count number of seeds in lateral branches and main stem at pod set, average of three plants per plot.

Total number of seeds on lateral branches at pod set [value/plant]—count total number of seeds on lateral branches at pod set, average of three plants per plot.

Total number of seeds on main stem at pod set [value/plant]—count total number of seeds on main stem at pod set, average of three plants per plot.

Plant height at pod set [cm/plant]—total length from above ground till the tip of the main stem at pod set, average of three plants per plot.

Plant height at harvest [cm/plant]—total length from above ground till the tip of the main stem at harvest, average of three plants per plot.

Total weight of pods on lateral branches at pod set [gr/plant]—weight of all pods on lateral branches at pod set, average of three plants per plot.

Ratio of the number of pods per node on main stem at pod set—calculated in formula XI, average of three plants per plot.

Formula XI: Total number of pods on main stem/Total number of nodes on main stem, average of three plants per plot.

Ratio of total number of seeds in main stem to number of seeds on lateral branches—calculated in formula XII, average of three plants per plot.

Formula XII: Total number of seeds on main stem at pod set/Total number of seeds on lateral branches at pod set.

Total weight of pods per plant at pod set [gr/plant]—weight all pods on lateral branches and main stem at pod set, average of three plants per plot.

Days till 50% flowering [days]—number of days till 50% flowering for each plot.

Days till 100% flowering [days]—number of days till 100% flowering for each plot.

Maturity [days]—measure as 95% of the pods in a plot have ripened (turned 100% brown). Delayed leaf drop and green stems are not considered in assigning maturity. Tests are observed 3 days per week, every other day, for maturity. The maturity date is the date that 95% of the pods have reached final color. Maturity is expressed in days after August 31 [according to the accepted definition of maturity in USA, Descriptor list for SOYBEAN, Hypertext Transfer Protocol://World Wide Web (dot) ars-grin (dot) gov/cgi-bin/npgs/html/desclist (dot) pl?51].

Seed quality [ranked 1-5]—measure at harvest, A visual estimate based on several hundred seeds. Parameter is rated according to the following scores considering the amount and degree of wrinkling, defective coat (cracks), greenishness, and moldy or other pigment. Rating is 1-very good, 2-good, 3-fair, 4-poor, 5-very poor.

Lodging [ranked 1-5]—is rated at maturity per plot according to the following scores: 1-most plants in a plot are erected, 2-All plants leaning slightly or a few plants down, 3-all plants leaning moderately, or 25%-50% down, 4-all plants leaning considerably, or 50%-80% down, 5-most plants down. Note: intermediate score such as 1.5 are acceptable.

Seed size [gr.]—weight of 1000 seeds per plot normalized to 13% moisture, measure at harvest.

Total weight of seeds per plant [gr./plant]—calculated at harvest (per 2 inner rows of a trimmed plot) as weight in grams of cleaned seeds adjusted to 13% moisture and divided by the total number of plants in two inner rows of a trimmed plot.

Yield at harvest [bushels/hectare]—calculated at harvest (per 2 inner rows of a trimmed plot) as weight in grams of cleaned seeds, adjusted to 13% moisture, and then expressed as bushels per acre.

Average lateral branch seeds per pod [number]—Calculate Num of Seeds on lateral branches-at pod set and divide by the Number of Total number of pods with seeds on lateral branches-at pod set.

Average main stem seeds per pod [number]—Calculate Total Number of Seeds on main stem at pod set and divide by the Number of Total number of pods with seeds on main stem at pod setting.

Main stem average internode length [cm]—Calculate Plant height at pod set and divide by the Total number of nodes on main stem at pod setting.

Total number of pods with seeds on main stem [number]—count all pods containing seeds on the main stem at pod setting.

Total number of pods with seeds on lateral branches [number]—count all pods containing seeds on the lateral branches at pod setting.

Total number of pods per plant at pod set [number]—count pods on main stem and lateral branches at pod setting.

Experimental Results

Twelve different Soybean varieties were grown and characterized for 40 parameters as specified in Table 39 below. The average for each of the measured parameters was calculated using the JMP software and values are summarized in Tables 40-41 below. Subsequent correlation analysis between the various transcriptom expression sets and the average parameters was conducted (Table 42). Results were then integrated to the database.

TABLE 39 Soybean correlated parameters (vectors) Correlation Correlated parameter with ID Base diameter at pod set (mm) 1 DW at pod set (gr.) 2 fresh weight at pod set (gr.) 3 Total number of nodes with pods on lateral branches 4 (number) Num of lateral branches (number) 5 Total weight of lateral branches at pod set (gr.) 6 Total weight of pods on main stem at pod set (gr.) 7 Total number of nodes on main stem (number) 8 Total no of pods with 1 seed on lateral branch (number) 9 Num of pods with 1 seed on main stem at pod set (number) 10 Total no of pods with 2 seed on lateral branch (number) 11 Num of pods with 2 seed on main stem (number) 12 Total no of pods with 3 seed on lateral branch (number) 13 Num of pods with 3 seed on main stem (number) 14 Total no of pods with 4 seed on lateral branch (number) 15 Num of pods with 4 seed on main stem (number) 16 Total number of seeds per plant 17 Total Number of Seeds on lateral branches 18 Total Number of Seeds on main stem at pod set 19 Plant height at pod set (cm) 20 Total weight of pods on lateral branches (gr.) 21 Ratio number of pods per node on main stem (ratio) 22 Ratio number of seeds per main stem to seeds per lateral 23 branch (ratio) Total weight of pods per plant (gr.) 24 50 percent flowering (days) 25 Maturity (days) 26 100 percent flowering (days) 27 Plant height at harvest (cm) 28 Seed quality (score 1-5) 29 Total weight of seeds per plant (gr./plant) 30 Seed size (gr.) 31 Lodging (score 1-5) 32 yield at harvest (bushel/hectare) 33 Average lateral branch seeds per pod (number) 34 Average main stem seeds per pod (number) 35 Total number of pods with seeds on main stem at pod set 36 (number) Num pods with seeds on lateral branches-at pod set 37 (number) Total number of pods per plant at pod set (number) 38 Main stem average internode length (cm/number) 39 Corrected Seed size (gr.) 40 Table 39.

TABLE 40 Measured parameters in Soybean varieties (lines1-6) Ecotype/ Correlation ID No. Line 1 Line 2 Line 3 Line 4 Line 5 Line 6 1 8.33 9.54 9.68 8.11 8.82 10.12 2 53.67 50.33 38.00 46.17 60.83 55.67 3 170.89 198.22 152.56 163.89 224.67 265.00 4 23.00 16.00 23.11 33.00 15.22 45.25 5 9.00 8.67 9.11 9.89 7.67 17.56 6 67.78 63.78 64.89 74.89 54.00 167.22 7 22.11 14.33 16.00 15.00 33.78 9.00 8 16.56 16.78 16.11 18.11 16.78 17.11 9 1.56 3.00 1.78 1.78 5.67 5.63 10 1.11 4.38 1.44 1.44 4.56 1.67 11 17.00 18.75 26.44 32.33 21.56 33.50 12 16.89 16.25 13.22 16.89 27.00 8.11 13 38.44 2.00 26.44 31.33 8.89 82.00 14 29.56 1.75 19.78 22.33 11.67 22.78 15 0.00 0.00 0.00 0.00 0.00 1.50 16 0.00 0.00 0.11 0.11 0.00 0.44 17 274.44 99.78 221.67 263.11 169.00 412.50 18 150.89 55.89 134.00 160.44 75.44 324.63 19 123.56 43.89 87.67 102.67 93.56 88.00 20 86.78 69.56 62.44 70.89 69.44 63.89 21 26.00 14.89 20.11 20.11 21.11 30.25 22 2.87 1.38 2.13 2.26 2.60 1.87 23 0.89 0.90 0.87 0.89 2.32 0.37 24 48.11 29.22 36.11 35.11 54.89 38.88 25 61.00 65.33 60.67 61.00 54.67 68.33 26 24.00 43.67 30.33 30.33 38.33 40.00 27 67.33 71.67 67.67 67.33 60.00 74.00 28 96.67 76.67 67.50 75.83 74.17 76.67 29 2.33 3.50 3.00 2.17 2.83 2.00 30 15.09 10.50 17.23 16.51 12.06 10.25 31 89.00 219.33 93.00 86.00 191.33 71.33 32 1.67 1.83 1.17 1.67 2.67 2.83 33 47.57 43.77 50.37 56.30 44.00 40.33 34 2.67 1.95 2.43 2.53 2.13 2.68 35 2.60 1.89 2.52 2.53 2.17 2.59 36 47.56 23.11 34.56 40.78 43.22 33.00 37 57.00 28.56 54.67 65.44 36.11 122.63 38 104.56 51.67 89.22 106.22 79.33 155.63 39 5.24 4.15 3.91 3.92 4.15 3.74 40 89.00 * 93.00 86.00 * 71.33 Table 40.

TABLE 41 Measured parameters in Soybean varieties (lines 7-12) Ecotype/ Correlation ID No. Line 7 Line 8 Line 9 Line 10 Line 11 Line 12 1 8.46 8.09 8.26 7.73 8.16 7.89 2 48.00 52.00 44.17 52.67 56.00 47.50 3 160.67 196.33 155.33 178.11 204.44 164.22 4 8.25 25.44 21.88 16.33 22.56 24.22 5 11.67 12.11 8.00 9.11 6.78 10.00 6 45.44 83.22 64.33 52.00 76.89 67.00 7 9.03 16.00 15.89 14.56 30.44 18.00 8 18.78 18.89 16.78 21.11 19.33 20.78 9 2.88 3.00 1.25 2.67 1.78 3.00 10 4.00 4.33 2.11 1.89 3.44 1.22 11 8.50 22.78 21.75 10.67 23.78 25.67 12 21.33 17.67 20.33 16.11 28.11 16.56 13 9.00 42.11 32.75 25.67 45.00 44.33 14 11.11 28.22 24.11 36.44 39.67 32.33 15 0.00 0.33 0.00 1.11 0.00 0.00 16 0.00 0.56 0.00 3.89 0.00 0.00 17 136.00 302.78 260.50 264.44 363.00 318.67 18 46.88 176.22 143.00 105.44 184.33 187.33 19 80.00 126.56 115.11 159.00 178.67 131.33 20 89.78 82.11 70.56 101.67 79.56 67.22 21 4.13 20.11 17.00 9.22 28.11 22.56 22 1.98 2.71 2.78 2.75 3.70 2.84 23 3.90 0.78 1.18 1.98 1.03 0.83 24 14.25 36.11 32.75 23.78 58.56 40.56 25 66.50 65.67 62.33 67.67 61.67 64.33 26 41.00 38.33 31.00 39.00 27.33 32.67 27 73.00 72.33 68.67 73.67 68.00 70.67 28 101.67 98.33 75.83 116.67 76.67 71.67 29 3.50 2.50 2.17 2.33 2.17 2.17 30 7.30 11.38 15.68 10.83 12.98 15.16 31 88.00 75.00 80.67 75.67 76.33 77.33 32 2.67 2.50 1.83 3.50 3.33 1.50 33 34.23 44.27 53.67 42.47 43.60 52.20 34 2.12 2.58 2.58 2.67 2.62 2.58 35 2.22 2.49 2.47 2.71 2.51 2.61 36 36.44 50.78 43.63 58.33 71.22 50.11 37 20.38 68.22 55.75 40.11 70.56 73.00 38 61.00 119.00 103.25 98.44 141.78 123.11 39 4.80 4.36 4.20 4.82 4.12 3.83 40 88.00 75.00 80.67 75.67 76.33 77.33 Table 41.

TABLE 42 Correlation between the expression level of selected genes of some embodiments of the invention in various tissues and the phenotypic performance under normal conditions across soybean varieties Gene Exp. Corr. Gene Exp. Corr. Name R P value set Set ID Name R P value set Set ID LYD437 0.71 2.10E−02 5 23 LYD437 0.76 2.79E−02 9 14 LYD437 0.84 9.58E−03 9 19 LYD437 0.85 7.25E−03 9 22 LYD437 0.73 7.53E−03 4 30 LYD437 0.71 9.26E−03 4 33 LYD438 0.86 1.38E−03 8 30 LYD438 0.81 4.31E−03 8 33 LYD438 0.71 1.02E−02 10 4 LYD438 0.71 9.94E−03 10 17 LYD439 0.79 6.84E−03 7 11 LYD439 0.74 1.43E−02 8 3 LYD439 0.79 7.01E−03 8 15 LYD439 0.72 2.01E−02 8 9 LYD439 0.82 4.05E−03 8 31 LYD439 0.78 2.19E−02 9 30 LYD439 0.73 3.97E−02 9 33 LYD439 0.75 3.09E−02 9 19 LYD439 0.82 1.18E−02 9 22 LYD439 0.72 4.40E−02 9 7 LYD439 0.76 6.38E−03 2 31 LYD439 0.71 1.02E−02 10 3 LYD440 0.84 2.29E−03 7 23 LYD440 0.78 8.30E−03 7 30 LYD440 0.76 1.02E−02 7 33 LYD440 0.73 1.67E−02 7 31 LYD440 0.76 4.52E−03 11 30 LYD440 0.79 2.22E−03 11 33 LYD440 0.81 4.12E−03 5 7 LYD440 0.76 1.04E−02 8 15 LYD440 0.71 4.81E−02 9 23 LYD440 0.75 3.33E−02 9 33 LYD440 0.76 2.84E−02 9 7 LYD440 0.74 8.79E−03 2 31 LYD440 0.79 2.00E−03 4 7 LYD441 0.71 2.10E−02 7 18 LYD441 0.80 5.65E−03 7 3 LYD441 0.87 9.46E−04 7 6 LYD441 0.77 9.62E−03 7 4 LYD441 0.76 4.21E−03 11 30 LYD441 0.83 7.65E−04 11 33 LYD441 0.75 1.26E−02 5 3 LYD441 0.83 2.98E−03 5 6 LYD441 0.91 2.85E−04 5 1 LYD441 0.72 1.88E−02 8 23 LYD441 0.81 1.42E−02 9 25 LYD441 0.84 8.80E−03 9 15 LYD441 0.71 5.03E−02 9 6 LYD441 0.93 8.95E−04 9 5 LYD441 0.77 2.44E−02 9 27 LYD441 0.83 1.08E−02 9 9 LYD441 0.81 2.55E−03 2 31 LYD441 0.77 3.63E−03 10 15 LYD442 0.77 3.12E−03 11 30 LYD442 0.86 3.26E−04 11 33 LYD442 0.82 1.23E−02 9 5 LYD442 0.80 1.92E−03 4 25 LYD442 0.78 2.57E−03 4 27 LYD443 0.74 1.49E−02 7 26 LYD443 0.77 8.47E−03 7 3 LYD443 0.78 7.44E−03 7 1 LYD443 0.81 4.94E−03 7 9 LYD443 0.78 3.05E−03 11 30 LYD443 0.76 4.41E−03 11 33 LYD443 0.77 8.92E−03 8 15 LYD443 0.71 2.04E−02 8 28 LYD443 0.73 1.60E−02 8 6 LYD443 0.83 3.21E−03 8 5 LYD443 0.80 1.64E−02 9 12 LYD443 0.77 2.49E−02 9 31 LYD443 0.80 2.99E−03 2 31 LYD443 0.74 5.78E−03 10 32 LYD445 0.74 1.39E−02 5 14 LYD445 0.89 5.63E−04 5 13 LYD445 0.88 8.05E−04 5 18 LYD445 0.80 5.31E−03 5 11 LYD445 0.80 5.46E−03 5 4 LYD445 0.94 7.06E−05 5 17 LYD445 0.71 2.28E−02 5 9 LYD445 0.77 9.00E−03 8 13 LYD445 0.77 8.50E−03 8 18 LYD445 0.72 1.84E−02 8 4 LYD445 0.73 1.62E−02 8 17 LYD445 0.87 5.49E−03 9 30 LYD445 0.75 3.37E−02 9 33 LYD445 0.73 3.82E−02 9 12 LYD445 0.80 1.61E−02 9 22 LYD445 0.74 3.72E−02 9 7 LYD445 0.75 4.89E−03 4 9 LYD445 0.74 6.41E−03 1 3 LYD445 0.80 1.66E−03 1 15 LYD445 0.76 3.95E−03 1 6 LYD445 0.71 9.11E−03 1 4 LYD445 0.80 1.87E−03 10 13 LYD445 0.76 3.87E−03 10 18 LYD445 0.83 8.99E−04 10 17 LYD446 0.92 1.56E−04 5 14 LYD446 0.90 4.07E−04 5 19 LYD446 0.75 1.29E−02 5 22 LYD446 0.77 9.54E−03 5 17 LYD446 0.71 2.07E−02 8 14 LYD446 0.71 2.21E−02 8 30 LYD446 0.84 2.62E−03 8 13 LYD446 0.85 1.64E−03 8 18 LYD446 0.76 1.05E−02 8 3 LYD446 0.84 2.44E−03 8 15 LYD446 0.92 1.63E−04 8 6 LYD446 0.73 1.65E−02 8 5 LYD446 0.89 5.06E−04 8 4 LYD446 0.74 1.35E−02 8 17 LYD446 0.72 4.46E−02 9 30 LYD446 0.76 2.75E−02 9 33 LYD446 0.73 7.17E−03 10 13 LYD446 0.76 3.96E−03 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LYD445 0.92 1.33E−04 5 38 LYD445 0.77 9.23E−03 8 37 LYD445 0.72 2.01E−02 8 35 LYD445 0.71 2.10E−02 8 38 LYD445 0.74 5.62E−03 10 37 LYD445 0.84 6.84E−04 10 38 LYD446 0.81 4.93E−03 5 35 LYD446 0.84 2.19E−03 5 36 LYD446 0.79 6.69E−03 5 34 LYD446 0.74 1.45E−02 5 38 LYD446 0.86 1.56E−03 8 37 LYD446 0.73 1.72E−02 8 35 LYD446 0.74 1.47E−02 8 34 LYD446 0.74 1.36E−02 8 38 LYD446 0.77 3.47E−03 10 37 LYD447 0.70 2.36E−02 5 37 LYD447 0.81 4.59E−03 5 38 LYD447 0.75 1.25E−02 8 37 LYD447 0.71 2.04E−02 8 35 LYD448 0.72 8.31E−03 10 37 LYD449 0.83 2.77E−03 5 37 LYD449 0.77 9.16E−03 5 38 LYD449 0.84 2.35E−03 8 37 LYD449 0.74 1.39E−02 8 38 LYD449 0.82 9.71E−04 10 37 LYD449 0.73 6.85E−03 10 38 LYD450 0.72 8.82E−03 10 38 LYD452 0.73 1.56E−02 5 37 LYD452 0.84 2.35E−03 8 37 LYD452 0.74 1.39E−02 8 38 LYD452 0.81 1.55E−03 10 37 LYD452 0.72 7.82E−03 10 38 LYD455 0.83 1.08E−02 9 36 LYD458 0.79 6.01E−03 8 35 LYD458 0.71 2.25E−02 8 34 LYD458 0.73 9.99E−03 2 35 LYD459 0.74 1.53E−02 7 37 LYD459 0.72 1.78E−02 7 35 LYD459 0.79 6.83E−03 7 34 LYD459 0.71 2.24E−02 7 38 LYD459 0.80 5.82E−03 5 37 LYD459 0.76 3.02E−02 9 37 LYD459 0.87 4.49E−04 2 35 LYD459 0.82 1.84E−03 2 34 LYD459 0.83 8.59E−04 10 37 LYD460 0.74 1.42E−02 5 37 LYD461 0.82 3.93E−03 5 36 LYD462 0.85 1.90E−03 8 37 LYD465 0.72 8.92E−03 10 37 LYD465 0.76 4.04E−03 10 34 LYD466 0.78 2.17E−02 9 37 LYD466 0.91 1.89E−03 9 35 LYD466 0.85 8.07E−03 9 34 LYD466 0.78 2.33E−02 9 38 LYD468 0.70 1.06E−02 1 34 LYD469 0.88 1.65E−04 1 36 LYD469 0.81 1.53E−03 10 37 LYD471 0.72 1.99E−02 8 35 LYD471 0.73 7.63E−03 10 37 LYD471 0.71 9.52E−03 10 35 LYD471 0.72 8.58E−03 10 34 LYD471 0.81 1.48E−03 10 38 LYD473 0.70 2.40E−02 8 35 LYD473 0.72 1.86E−02 8 34 LYD511 0.72 4.53E−02 9 37 LYD513 0.92 1.56E−04 7 35 LYD513 0.90 3.48E−04 7 34 LYD513 0.72 1.82E−02 7 38 LYD514 0.75 1.24E−02 8 35 LYD514 0.74 5.59E−03 4 36 LYD515 0.79 2.45E−03 10 36 LYD516 0.72 4.34E−02 9 37 LYD516 0.75 4.91E−03 10 37 LYD516 0.71 9.74E−03 10 38 LYD517 0.72 1.83E−02 7 36 LYD517 0.81 4.61E−03 8 37 LYD517 0.78 7.26E−03 8 38 LYD517 0.86 6.47E−03 9 37 LYD517 0.79 1.93E−02 9 38 LYD518 0.81 1.40E−03 11 36 LYD518 0.80 5.27E−03 5 37 LYD519 0.81 4.93E−03 5 35 LYD519 0.84 2.19E−03 5 36 LYD519 0.80 5.26E−03 5 34 LYD519 0.87 9.29E−04 5 38 LYD519 0.93 8.53E−05 8 37 LYD519 0.79 6.99E−03 8 38 LYD519 0.74 6.38E−03 10 37 LYD437 0.74 3.55E−02 7 40 LYD438 0.74 3.46E−02 7 40 LYD438 0.79 6.15E−03 4 40 LYD438 0.71 2.21E−02 1 40 LYD440 0.74 5.82E−02 9 40 LYD440 0.72 1.90E−02 10 40 LYD447 0.71 2.25E−02 11 40 LYD447 0.72 1.97E−02 1 40 LYD448 0.78 2.31E−02 5 40 LYD449 0.83 1.02E−02 7 40 LYD449 0.76 1.77E−02 2 40 LYD449 0.77 9.76E−03 4 40 LYD455 0.73 1.62E−02 11 40 LYD465 0.73 6.40E−02 9 40 LYD514 0.73 1.71E−02 1 40 LYD517 0.74 1.47E−02 11 40 Table 42. Provided are the correlations (R) between the expression levels yield improving genes and their homologs in various tissues [Expression (Exp) sets] and the phenotypic performance [yield, biomass, and plant architecture (Correlation vector (Corr.) ID)] under normal conditions across soybean varieties. P = p value.

Example 10 Production of Barley Transcriptom and High Throughput Correlation Analysis Using 44K Barley Oligonucleotide Micro-Array

In order to produce a high throughput correlation analysis, the present inventors utilized a Barley oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp?1Page=50879]. The array oligonucleotide represents about 47,500 Barley genes and transcripts. In order to define correlations between the levels of RNA expression and yield or vigor related parameters, various plant characteristics of 25 different Barley accessions were analyzed. Among them, 13 accessions encompassing the observed variance were selected for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html].

Experimental Procedures

Five tissues at different developmental stages [meristem, flower, booting spike, stem, flag leaf], representing different plant characteristics, were sampled and RNA was extracted as described hereinabove under “GENERAL EXPERIMENTAL AND BIOINFORMATICS METHODS”.

For convenience, each micro-array expression information tissue type has received a Set ID as summarized in Table 43 below.

TABLE 43 Barley transcriptom expression sets Expression Set Set ID booting spike at flowering stage 1 Stem at flowering stage 2 flowering spike at flowering stage 3 Meristem at flowering stage 4 Table 43: Provided are the identification (ID) digits of each of the Barley expression sets.

Barley yield components and vigor related parameters assessment—13 Barley accessions in 4 repetitive blocks (named A, B, C, and D), each containing 4 plants per plot were grown at net house. Plants were phenotyped on a daily basis following the standard descriptor of barley (Table 44, below). Harvest was conducted while 50% of the spikes were dry to avoid spontaneous release of the seeds. Plants were separated to the vegetative part and spikes, of them, 5 spikes were threshed (grains were separated from the glumes) for additional grain analysis such as size measurement, grain count per spike and grain yield per spike. All material was oven dried and the seeds were threshed manually from the spikes prior to measurement of the seed characteristics (weight and size) using scanning and image analysis. The image analysis system included a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.37 (Java based image processing program, which was developed at the U.S. National Institutes of Health and freely available on the internet [Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute).

TABLE 44 Barley standard descriptors Trait Parameter Range Description Growth habit Scoring 1-9 Prostrate (1) or Erect (9) Hairiness of Scoring P (Presence)/ Absence (1) or basal leaves A (Absence) Presence (2) Stem Scoring 1-5 Green (1), Basal only or pigmentation Half or more (5) Days to Days Days from sowing to Flowering emergence of awns Plant height Centimeter Height from ground level (cm) to top of the longest spike excluding awns Spikes per Number Terminal Counting plant Spike length Centimeter Terminal Counting (cm) 5 spikes per plant Grains per Number Terminal Counting spike 5 spikes per plant Vegetative Gram Oven-dried for 48 hours dry weight at 70° C. Spikes dry Gram Oven-dried for 48 hours weight at 30° C. Table 44.

At the end of the experiment (50% of the spikes were dry) all spikes from plots within blocks A-D were collected, and the following measurements were performed:

(i) Grains per spike—The total number of grains from 5 spikes that were manually threshed was counted. The average grain per spike was calculated by dividing the total grain number by the number of spikes.

(ii) Grain average size (cm)—The total grains from 5 spikes that were manually threshed were scanned and images were analyzed using the digital imaging system. Grain scanning was done using Brother scanner (model DCP-135), at the 200 dpi resolution and analyzed with Image J software. The average grain size was calculated by dividing the total grain size by the total grain number.

(iii) Grain average weight (mgr)—The total grains from 5 spikes that were manually threshed were counted and weight. The average weight was calculated by dividing the total weight by the total grain number.

(iv) Grain yield per spike (gr)—The total grains from 5 spikes that were manually threshed were weight. The grain yield was calculated by dividing the total weight by the spike number.

(v) Spike length analysis—The five chosen spikes per plant were measured using measuring tape excluding the awns.

(vi) Spike number analysis—The spikes per plant were counted.

Additional parameters were measured as follows: Growth habit scoring—At growth stage 10 (booting), each of the plants was scored for its growth habit nature. The scale that was used was 1 for prostate nature till 9 for erect.

Hairiness of basal leaves—At growth stage 5 (leaf sheath strongly erect; end of tillering), each of the plants was scored for its hairiness nature of the leaf before the last. The scale that was used was 1 for prostate nature till 9 for erect.

Plant height—At harvest stage (50% of spikes were dry), each of the plants was measured for its height using measuring tape. Height was measured from ground level to top of the longest spike excluding awns.

Days to flowering—Each of the plants was monitored for flowering date. Days of flowering was calculated from sowing date till flowering date.

Stem pigmentation—At growth stage 10 (booting), each of the plants was scored for its stem color. The scale that was used was 1 for green till 5 for full purple.

Vegetative dry weight and spike yield—At the end of the experiment (50% of the spikes were dry) all spikes and vegetative material from plots within blocks A-D are collected. The biomass and spikes weight of each plot was separated, measured and divided by the number of plants.

Dry weight=total weight of the vegetative portion above ground (excluding roots) after drying at 70° C. in oven for 48 hours;

Spike yield per plant=total spike weight per plant (gr.) after drying at 30° C. in oven for 48 hours.

TABLE 45 Barley correlated parameters (vectors) Correlation Correlated parameter with ID Spikes per plant (number) 1 days to flowering (days) 2 Grain weight (gr) 3 Spike length (cm) 4 Grains Size (mm) 5 Grains per spike (number) 6 Growth habit (score 1-9) 7 Hairiness of basal leaves (score 1-9) 8 Plant height (cm) 9 Seed Yield of 5 Spikes (gr.) 10 Stem pigmentation (score 1-5) 11 Vegetative dry weight (gr.) 12 Table 45. Provided are the Barley correlated parameters (vectors).

Experimental Results

13 different Barley accessions were grown and characterized for 12 parameters as described above. The average for each of the measured parameter was calculated using the JMP software and values are summarized in Tables 46 and 47 below. Subsequent correlation analysis between the various transcriptom expression sets (Table 43) and the average parameters (Tables 46-47) was conducted. Follow, results were integrated to the database (Table 48 below).

TABLE 46 Measured parameters of correlation Ids in Barley accessions (lines 1-6) Ecotype/ Correlation ID No. Line-1 Line-2 Line-3 Line-4 Line-5 Line-6 1 48.846 48.273 37.417 61.917 33.273 41.692 2 62.400 64.083 65.154 58.917 63.000 70.538 3 35.046 28.065 28.761 17.869 41.216 29.734 4 12.036 10.932 11.825 9.900 11.682 11.532 5 0.265 0.229 0.244 0.166 0.295 0.275 6 20.229 17.983 17.267 17.733 14.467 16.783 7 2.600 2.000 1.923 3.167 4.333 2.692 8 1.533 1.333 1.692 1.083 1.417 1.692 9 134.267 130.500 138.769 114.583 127.750 129.385 10 3.559 2.538 2.583 1.574 3.030 2.517 11 1.133 2.500 1.692 1.750 2.333 2.308 12 78.871 66.141 68.491 53.389 68.300 74.173 Table 46. Provided are the values of each of the parameters measured in Barley accessions according to the correlation identifications (see Table 45).

TABLE 47 Barley accessions, additional measured parameters (lines 7-13) Ecotype/ Correlation ID No. Line-7 Line-8 Line-9 Line-10 Line-11 Line-12 Line-13 1 40.000 40.625 62.000 49.333 50.600 43.091 51.400 2 52.800 60.875 58.100 53.000 60.400 64.583 56.000 3 25.224 34.994 20.580 27.501 37.126 29.564 19.583 4 8.863 11.216 11.108 8.583 10.179 10.505 9.803 5 0.220 0.278 0.187 0.224 0.273 0.271 0.179 6 12.120 14.067 21.540 12.100 13.400 15.283 17.067 7 3.600 3.500 3.000 3.667 2.467 3.500 3.000 8 1.300 1.188 1.000 1.167 1.600 1.083 1.167 9 103.889 121.625 126.800 99.833 121.400 118.417 117.167 10 1.549 2.624 2.300 1.678 2.677 2.353 1.673 11 1.700 2.188 2.300 1.833 3.067 1.583 2.167 12 35.354 58.334 62.230 38.322 68.306 56.148 42.682 Table 47. Provided are the values of each of the parameters measured in Barley accessions according to the correlation identifications (see Table 45).

TABLE 48 Correlation between the expression level of the selected polynucleotides of the invention and their homologues in specific tissues or developmental stages and the phenotypic performance across Barley accessions Corr. Corr. Gene Exp. Set Gene Exp. Set Name R P value set ID Name R P value set ID LYD370 0.71 4.80E−02 4 1 LYD371 0.78 2.21E−02 4 1 Table 48. Provided are the correlations (R) between the expression levels yield improving genes and their homologs in various tissues [Expression (Exp) sets] and the phenotypic performance (Correlation vector (Corr.) ID)] under normal conditions across barley varieties. P = p value.

Example 11 Production of Cotton Transcriptom and High Throughput Correlation Analysis for Plant Fiber Development Using Cotton Oligonucleotide Microarray

In order to conduct high throughput gene expression correlation analysis, the present inventors used cotton oligonucleotide microarray, designed and produced by “Comparative Evolutionary Genomics of Cotton” [Hypertext Transfer Protocol www (dot) cottonevolution (dot) info/). This Cotton Oligonucleotide Microarray is composed of 12,006 Integrated DNA Technologies (IDT) oligonucleotides derived from an assembly of more than 180,000 Gossypium ESTs sequenced from 30 cDNA libraries. For additional details see PCT/IL2005/000627 and PCT/IL2007/001590 which are fully incorporated herein by reference.

TABLE 49 Cotton transcriptom experimental sets Expression Set Set ID cotton fiber length 15 days post anthesis 1 cotton fiber length 5 days post 2 cotton fiber length 10 days post anthesis 3 Table 49. Provided are the cotton transcriptom expression sets.

In order to define correlations between the levels of RNA expression and fiber length, fibers from 8 different cotton lines were analyzed. These fibers were selected showing very good fiber quality and high lint index (Pima types, originating from other cotton species, namely G. barbadense), different levels of quality and lint indexes from various G. hirsutum lines: good quality and high lint index (Acala type), and poor quality and short lint index (Tamcot type, and old varieties). A summary of the fiber length of the different lines is provided in Table 51.

Experimental Procedures

RNA extraction—Fiber development stages, representing different fiber characteristics, at 5, 10 and 15 DPA (Days After Anthesis) were sampled and RNA was extracted as described above.

Fiber length assessment—Fiber length of the selected cotton lines was measured using fibrograph. The fibrograph system was used to compute length in terms of “Upper Half Mean” length. The upper half mean (UHM) is the average length of longer half of the fiber distribution. The fibrograph measures length in span lengths at a given percentage point World Wide Web (dot) cottoninc (dot) com/ClassificationofCotton/?Pg=4#Length].

Experimental Results

Eight different cotton lines were grown, and their fiber length was measured. The fibers UHM values are summarized in Table 51 herein below. The correlation between expression level of genes of some embodiments of the invention and cotton fiber length under normal growth conditions was performed (Table 52).

TABLE 50 Cotton correlation parameter Correlated parameter with Correlation ID Fiber Length 1 Table 50.

TABLE 51 Summary of the fiber length (UHM) of the 8 different cotton lines Correlation ID No./Ecotype 1 Line-1 1.21 Line-2 1.1 Line-3 1.36 Line-4 1.26 Line-5 0.89 Line-6 1.01 Line-7 1.06 Line-8 1.15 Table 51: Presented are the UHM of 8 different cotton lines.

TABLE 52 Correlation between the expression level of selected LYD genes of some embodiments of the invention in various tissues and cotton fiber length under normal growth conditions in cotton Corr. Corr. Gene Exp. Set Gene Exp. Set Name R P value set ID Name R P value set ID LYD380 0.84 1.92E−02 3 1 LYD382 0.79 1.92E−02 2 1 LYD382 0.87 1.08E−02 3 1 LYD383 0.72 4.20E−02 1 1 LYD385 0.77 2.52E−02 1 1 LYD386 0.76 2.70E−02 2 1 LYD386 0.77 4.35E−02 3 1 LYD387 0.84 9.34E−03 1 1 LYD388 0.88 9.63E−03 3 1 LYD502 0.73 6.19E−02 3 1 Table 52. Provided are the correlations between the expression level of the genes and the effect on fiber length. “Exp. Set”—Expression set. “R” = Pearson correlation coefficient; “P” = p value.

Example 12 Identification of Genes which Increase Yield, Biomass, Growth Rate, Vigor, Oil Content, Abiotic Stress Tolerance of Plants and Nitrogen Use Efficiency

Based on the above described bioinformatics and experimental tools, the present inventors have identified 201 genes which have a major impact on yield, seed yield, oil yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or fertilizer (e.g., nitrogen) use efficiency when expression thereof is increased in plants. The identified genes (including genes identified by bioinformatics tools, variants, curated sequences thereof and cloned sequences), and polypeptide sequences encoded thereby are summarized in Table 53, hereinbelow.

TABLE 53 Identified polynucleotides which affect plant yield, seed yield, oil yield, oil content, biomass, growth rate, vigor, fiber yield, fiber quality abiotic stress tolerance and/or nitrogen use efficiency of a plant Polyn. Polyp. SEQ SEQ Gene ID ID Name Cluster Name Organism NO: NO: LYD289 arabidopsis|10v1|AT1G02040 arabidopsis 1 456 LYD290 arabidopsis|10v1|AT1G09560 arabidopsis 2 457 LYD291 arabidopsis|10v1|AT1G10970 arabidopsis 3 458 LYD292 arabidopsis|10v1|AT1G13740 arabidopsis 4 459 LYD293 arabidopsis|10v1|AT1G14620 arabidopsis 5 460 LYD294 arabidopsis|10v1|AT1G27300 arabidopsis 6 461 LYD295 arabidopsis|10v1|AT1G27900 arabidopsis 7 462 LYD296 arabidopsis|10v1|AT1G30820 arabidopsis 8 463 LYD297 arabidopsis|10v1|AT1G51440 arabidopsis 9 464 LYD298 arabidopsis|10v1|AT1G55910 arabidopsis 10 465 LYD299 arabidopsis|10v1|AT1G61600 arabidopsis 11 466 LYD300 arabidopsis|10v1|AT1G61790 arabidopsis 12 467 LYD301 arabidopsis|10v1|AT1G74790 arabidopsis 13 468 LYD302 arabidopsis|10v1|AT1G77060 arabidopsis 14 469 LYD303 arabidopsis|10v1|AT2G01710 arabidopsis 15 470 LYD304 arabidopsis|10v1|AT2G03810 arabidopsis 16 471 LYD305 arabidopsis|10v1|AT2G05220 arabidopsis 17 472 LYD306 arabidopsis|10v1|AT2G07674 arabidopsis 18 473 LYD307 arabidopsis|10v1|AT2G17990 arabidopsis 19 474 LYD308 arabidopsis|10v1|AT2G37478 arabidopsis 20 475 LYD309 arabidopsis|10v1|AT2G40020 arabidopsis 21 476 LYD310 arabidopsis|10v1|AT2G40300 arabidopsis 22 477 LYD311 arabidopsis|10v1|AT2G40510 arabidopsis 23 478 LYD312 arabidopsis|10v1|AT2G42770 arabidopsis 24 479 LYD313 arabidopsis|10v1|AT3G04620 arabidopsis 25 480 LYD315 arabidopsis|10v1|AT3G05390 arabidopsis 26 481 LYD316 arabidopsis|10v1|AT3G09030 arabidopsis 27 482 LYD318 arabidopsis|10v1|AT3G11900 arabidopsis 28 483 LYD319 arabidopsis|10v1|AT3G14070 arabidopsis 29 484 LYD320 arabidopsis|10v1|AT3G15810 arabidopsis 30 485 LYD321 arabidopsis|10v1|AT3G18750 arabidopsis 31 486 LYD322 arabidopsis|10v1|AT3G21190 arabidopsis 32 487 LYD323 arabidopsis|10v1|AT3G44280 arabidopsis 33 488 LYD324 arabidopsis|10v1|AT3G47860 arabidopsis 34 489 LYD325 arabidopsis|10v1|AT3G49390 arabidopsis 35 490 LYD326 arabidopsis|10v1|AT3G49490 arabidopsis 36 491 LYD327 arabidopsis|10v1|AT3G51895 arabidopsis 37 492 LYD328 arabidopsis|10v1|AT3G59210 arabidopsis 38 493 LYD329 arabidopsis|10v1|AT3G62270 arabidopsis 39 494 LYD330 arabidopsis|10v1|AT4G13070 arabidopsis 40 495 LYD331 arabidopsis|10v1|AT4G17440 arabidopsis 41 496 LYD332 arabidopsis|10v1|AT4G35110 arabidopsis 42 497 LYD334 arabidopsis|10v1|AT5G03870 arabidopsis 43 498 LYD335 arabidopsis|10v1|AT5G04140 arabidopsis 44 499 LYD337 arabidopsis|10v1|AT5G11740 arabidopsis 45 500 LYD338 arabidopsis|10v1|AT5G12410 arabidopsis 46 501 LYD339 arabidopsis|10v1|AT5G13560 arabidopsis 47 502 LYD340 arabidopsis|10v1|AT5G16420 arabidopsis 48 503 LYD341 arabidopsis|10v1|AT5G36700 arabidopsis 49 504 LYD342 arabidopsis|10v1|AT5G44680 arabidopsis 50 505 LYD343 arabidopsis|10v1|AT5G46150 arabidopsis 51 506 LYD344 arabidopsis|10v1|AT5G64840 arabidopsis 52 507 LYD346 b_juncea|10v2|BJ1SLX00003156 b_juncea 53 508 LYD347 b_juncea|10v2|BJ1SLX00219277D1 b_juncea 54 509 LYD348 b_juncea|10v2|BJ1SLX01241733D1 b_juncea 55 510 LYD349 b_juncea|10v2|E6ANDIZ01A0PVA b_juncea 56 511 LYD351 b_juncea|10v2|E6ANDIZ01A2WXZ b_juncea 57 512 LYD352 b_juncea|10v2|E6ANDIZ01A7124 b_juncea 58 513 LYD353 b_juncea|10v2|E6ANDIZ01AK44C b_juncea 59 514 LYD354 b_juncea|10v2|E6ANDIZ01ALST2 b_juncea 60 515 LYD355 b_juncea|10v2|E6ANDIZ01AM1M7 b_juncea 61 516 LYD356 b_juncea|10v2|E6ANDIZ01AR3Y3 b_juncea 62 517 LYD357 b_juncea|10v2|E6ANDIZ01AU0CH b_juncea 63 518 LYD358 b_juncea|10v2|E6ANDIZ01AUG5K b_juncea 64 519 LYD359 b_juncea|10v2|E6ANDIZ01AVIGM b_juncea 65 520 LYD360 b_juncea|10v2|E6ANDIZ01BHOKJ b_juncea 66 521 LYD361 b_juncea|10v2|E6ANDIZ01BIDFA b_juncea 67 522 LYD362 b_juncea|10v2|E6ANDIZ01C68KB b_juncea 68 523 LYD364 b_juncea|10v2|E6ANDIZ01ET44E b_juncea 69 524 LYD365 b_juncea|10v2|E6ANDIZ01EWUI0 b_juncea 70 525 LYD366 b_juncea|10v2|E6ANDIZ02FS13L b_juncea 71 526 LYD367 b_juncea|10v2|E6ANDIZ02GKPXS b_juncea 72 527 LYD368 b_juncea|10v2| b_juncea 73 528 OXBJ1SLX00002741D1T1 LYD370 barley|10v2|AV834829 barley 74 529 LYD371 barley|10v2|BJ450532 barley 75 530 LYD372 canola|10v1|CD828626 canola 76 531 LYD375 canola|10v1|DY011663 canola 77 532 LYD376 canola|10v1|ES964015 canola 78 533 LYD377 canola|10v1|EV098360 canola 79 534 LYD378 canola|10v1|EV114958 canola 80 535 LYD379 canola|10v1|EV129887 canola 81 536 LYD380 cotton|10v1barbadense|BE054896 cotton 82 537 LYD381 cotton|10v1|AI727565 cotton 83 538 LYD382 cotton|10v2|AI726887 cotton 84 539 LYD383 cotton|10v2|BG447338 cotton 85 540 LYD385 cotton|10v2|DN799940 cotton 86 541 LYD386 cotton|10v2|DN804420 cotton 87 542 LYD387 cotton|10v2|DT466425 cotton 88 543 LYD388 cotton|10v2|EX167553 cotton 89 544 LYD390 cotton|gb164|AI055341 cotton 90 545 LYD391 maize|10v1|AA011869 maize 91 546 LYD392 maize|10v1|BE512624 maize 92 547 LYD393 medicago|09v1|AI974481 medicago 93 548 LYD395 medicago|09v1|AL379818 medicago 94 549 LYD396 medicago|09v1|AW256719 medicago 95 550 LYD397 medicago|09v1|AW257291 medicago 96 551 LYD398 medicago|09v1|AW329709 medicago 97 552 LYD399 medicago|09v1|AW688882 medicago 98 553 LYD401 medicago|09v1|AW690536 medicago 99 554 LYD402 medicago|09v1|AW694333 medicago 100 555 LYD403 medicago|09v1|AW698677 medicago 101 556 LYD404 medicago|09v1|AW736500 medicago 102 557 LYD405 medicago|09v1|AW775077 medicago 103 558 LYD407 medicago|09v1|BE322971 medicago 104 559 LYD408 medicago|09v1|BE324051 medicago 105 560 LYD409 medicago|09v1|BF521188 medicago 106 561 LYD410 medicago|09v1|BG452469 medicago 107 562 LYD413 medicago|09v1|BQ124797 medicago 108 563 LYD414 medicago|09v1|BQ157221 medicago 109 564 LYD415 medicago|09v1|CX516971 medicago 110 565 LYD416 medicago|09v1|LLAJ388869 medicago 111 566 LYD417 medicago|09v1|LLAL373168 medicago 112 567 LYD418 medicago|09v1|LLAW688750 medicago 113 568 LYD419 medicago|09v1|LLAW698759 medicago 114 569 LYD420 medicago|09v1|LLAW776476 medicago 115 570 LYD421 medicago|09v1|LLBI271813 medicago 116 571 LYD422 medicago|09v1|MT454X026824 medicago 117 572 LYD423 sorghum|09v1|SB01G027910 sorghum 118 573 LYD424 sorghum|09v1|SB01G046300 sorghum 119 574 LYD425 sorghum|09v1|SB02G004290 sorghum 120 575 LYD427 sorghum|09v1|SB03G025240 sorghum 121 576 LYD428 sorghum|09v1|SB04G002930 sorghum 122 577 LYD431 sorghum|09v1|SB05G020810 sorghum 123 578 LYD432 sorghum|09v1|SB06G021780 sorghum 124 579 LYD433 sorghum|09v1|SB07G014630 sorghum 125 580 LYD434 sorghum|09v1|SB07G019310 sorghum 126 581 LYD435 sorghum|09v1|SB07G019840 sorghum 127 582 LYD436 sorghum|09v1|SB09G003870 sorghum 128 583 LYD437 soybean|11v1|GLYMA01G09460 soybean 129 584 LYD438 soybean|11v1|GLYMA02G33320 soybean 130 585 LYD439 soybean|11v1|GLYMA03G34340 soybean 131 586 LYD440 soybean|11v1|GLYMA03G40870 soybean 132 587 LYD441 soybean|11v1|GLYMA04G36500 soybean 133 588 LYD442 soybean|11v1|GLYMA04G39480 soybean 134 589 LYD443 soybean|11v1|GLYMA04G41020 soybean 135 590 LYD445 soybean|11v1|GLYMA06G03510 soybean 136 591 LYD446 soybean|11v1|GLYMA06G17910 soybean 137 592 LYD447 soybean|11v1|GLYMA07G07150 soybean 138 593 LYD448 soybean|11v1|GLYMA07G08010 soybean 139 594 LYD449 soybean|11v1|GLYMA07G10060 soybean 140 595 LYD450 soybean|11v1|GLYMA09G26770 soybean 141 596 LYD451 soybean|11v1|GLYMA09G29610 soybean 142 597 LYD452 soybean|11v1|GLYMA09G31720 soybean 143 598 LYD453 soybean|11v1|GLYMA11G01120 soybean 144 599 LYD454 soybean|11v1|GLYMA11G03570 soybean 145 600 LYD455 soybean|11v1|GLYMA11G11560 soybean 146 601 LYD456 soybean|11v1|GLYMA12G01770 soybean 147 602 LYD458 soybean|11v1|GLYMA13G22110 soybean 148 603 LYD459 soybean|11v1|GLYMA13G23920 soybean 149 604 LYD460 soybean|11v1|GLYMA13G28620 soybean 150 605 LYD461 soybean|11v1|GLYMA15G37980 soybean 151 606 LYD462 soybean|11v1|GLYMA16G04350 soybean 152 607 LYD465 soybean|11v1|GLYMA17G18250 soybean 153 608 LYD466 soybean|11v1|GLYMA18G49340 soybean 154 609 LYD467 soybean|11v1|GLYMA19G14700 soybean 155 610 LYD468 soybean|11v1|GLYMA19G36240 soybean 156 611 LYD469 soybean|11v1|GLYMA19G38830 soybean 157 612 LYD470 soybean|11v1|GLYMA19G43610 soybean 158 613 LYD471 soybean|11v1|GLYMA20G38820 soybean 159 614 LYD472 soybean|gb168|AW348492 soybean 160 615 LYD473 soybean|gb168|BE661322 soybean 161 616 LYD474 sunflower|10v1|CD849185 sunflower 162 617 LYD475 tomato|09v1|AI485596 tomato 163 618 LYD477 tomato|09v1|BP884530 tomato 164 619 LYD478 tomato|10v1|AI483112 tomato 165 620 LYD479 tomato|10v1|AI484249 tomato 166 621 LYD480 tomato|10v1|AI771275 tomato 167 622 LYD481 tomato|10v1|AI771986 tomato 168 623 LYD482 tomato|10v1|AI777950 tomato 169 624 LYD483 tomato|10v1|AW738746 tomato 170 625 LYD484 tomato|10v1|AW929870 tomato 171 626 LYD487 tomato|10v1|BG127385 tomato 172 627 LYD489 tomato|10v1|BG131472 tomato 173 628 LYD491 tomato|10v1|BM061560 tomato 174 629 LYD492 tomato|10v1|DB714406 tomato 175 630 LYD495 wheat|gb164|BG604441 wheat 176 631 LYD497 b_juncea|10v2|E6ANDIZ01AJCUK b_juncea 177 632 LYD498 b_juncea|10v2|E6ANDIZ01AJQJC b_juncea 178 633 LYD499 b_juncea|10v2|E6ANDIZ01B9PEA b_juncea 179 634 LYD500 b_juncea|10v2|E6ANDIZ02FZU2Y2 b_juncea 180 635 LYD501 b_juncea|10v2|E6ANDIZ02G70KP b_juncea 181 636 LYD502 cotton|10v2|DW503396 cotton 182 637 LYD503 maize|10v1|AI637036 maize 183 638 LYD504 medicago|09v1|AA660909 medicago 184 639 LYD505 medicago|09v1|AJ388789 medicago 185 640 LYD506 medicago|09v1|BE239698 medicago 186 641 LYD507 sorghum|09v1|SB01G017330 sorghum 187 642 LYD508 sorghum|09v1|SB02G014460 sorghum 188 643 LYD509 sorghum|09v1|SB02G028300 sorghum 189 644 LYD510 sorghum|09v1|SB09G025320 sorghum 190 645 LYD511 soybean|11v1|BE660230 soybean 191 646 LYD512 soybean|11v1|GLYMA03G36420 soybean 192 647 LYD513 soybean|11v1|GLYMA03G39480 soybean 193 648 LYD514 soybean|11v1|GLYMA05G04990 soybean 194 649 LYD515 soybean|11v1|GLYMA07G36970 soybean 195 650 LYD516 soybean|11v1|GLYMA13G24040 soybean 196 651 LYD517 soybean|11v1|GLYMA15G06930 soybean 197 652 LYD518 soybean|11v1|GLYMA18G48880 soybean 198 653 LYD519 soybean|gb168|AW686841 soybean 199 654 LYD520 soybean|gb168|FG994976 soybean 200 655 LYD496 arabidopsis|10v1|AT1G58235 arabidopsis 201 — LYD299 arabidopsis|10v1|AT1G61600 arabidopsis 202 466 LYD331 arabidopsis|10v1|AT4G17440 arabidopsis 203 496 LYD340 arabidopsis|10v1|AT5G16420 arabidopsis 204 503 LYD372 canola|10v1|CD828626 canola 225 531 LYD379 canola|10v1|EV129887 canola 229 536 LYD420 medicago|09v1|LLAW776476 medicago 237 570 LYD477 tomato|09v1|BP884530 tomato 248 619 LYD479 tomato|10v1|AI484249 tomato 249 621 LYD489 tomato|10v1|BG131472 tomato 251 628 LYD346 b_juncea|10v2|BJ1SLX00003156 b_juncea 205 656 LYD347 b_juncea|10v2|BJ1SLX00219277D1 b_juncea 206 657 LYD348 b_juncea|10v2|BJ1SLX01241733D1 b_juncea 207 658 LYD349 b_juncea|10v2|E6ANDIZ01A0PVA b_juncea 208 659 LYD351 b_juncea|10v2|E6ANDIZ01A2WXZ b_juncea 209 660 LYD352 b_juncea|10v2|E6ANDIZ01A7124 b_juncea 210 661 LYD353 b_juncea|10v2|E6ANDIZ01AK44C b_juncea 211 662 LYD354 b_juncea|10v2|E6ANDIZ01ALST2 b_juncea 212 663 LYD355 b_juncea|10v2|E6ANDIZ01AM1M7 b_juncea 213 664 LYD356 b_juncea|10v2|E6ANDIZ01AR3Y3 b_juncea 214 665 LYD357 b_juncea|10v2|E6ANDIZ01AU0CH b_juncea 215 666 LYD358 b_juncea|10v2|E6ANDIZ01AUG5K b_juncea 216 667 LYD359 b_juncea|10v2|E6ANDIZ01AVIGM b_juncea 217 668 LYD360 b_juncea|10v2|E6ANDIZ01BHOKJ b_juncea 218 669 LYD361 b_juncea|10v2|E6ANDIZ01BIDFA b_juncea 219 670 LYD364 b_juncea|10v2|E6ANDIZ01ET44E b_juncea 220 671 LYD365 b_juncea|10v2|E6ANDIZ01EWUI0 b_juncea 221 672 LYD366 b_juncea|10v2|E6ANDIZ02FS13L b_juncea 222 673 LYD367 b_juncea|10v2|E6ANDIZ02GKPXS b_juncea 223 674 LYD371 barley|10v2|BJ450532 barley 224 675 LYD376 canola|10v1|ES964015 canola 226 676 LYD377 canola|10v1|EV098360 canola 227 677 LYD378 canola|10v1|EV114958 canola 228 678 LYD380 cotton|10v1barbadense|BE054896 cotton 230 679 LYD383 cotton|10v2|BG447338 cotton 231 680 LYD388 cotton|10v2|EX167553 cotton 232 681 LYD390 cotton|gb164|AI055341 cotton 233 682 LYD413 medicago|09v1|BQ124797 medicago 234 683 LYD417 medicago|09v1|LLAL373168 medicago 235 684 LYD418 medicago|09v1|LLAW688750 medicago 236 685 LYD421 medicago|09v1|LLBI271813 medicago 238 686 LYD422 medicago|09v1|MT454X026824 medicago 239 687 LYD431 sorghum|09v1|SB05G020810 sorghum 240 688 LYD434 sorghum|09v1|SB07G019310 sorghum 241 689 LYD443 soybean|11v1|GLYMA04G41020 soybean 242 690 LYD446 soybean|11v1|GLYMA06G17910 soybean 243 691 LYD448 soybean|11v1|GLYMA07G08010 soybean 244 692 LYD458 soybean|11v1|GLYMA13G22110 soybean 245 693 LYD461 soybean|11v1|GLYMA15G37980 soybean 246 694 LYD471 soybean|11v1|GLYMA20G38820 soybean 247 695 LYD483 tomato|10v1|AW738746 tomato 250 696 LYD495 wheat|gb164|BG604441 wheat 252 697 LYD497 b_juncea|10v2|E6ANDIZ01AJCUK b_juncea 253 698 LYD499 b_juncea|10v2|E6ANDIZ01B9PEA b_juncea 254 699 LYD500 b_juncea|10v2|E6ANDIZ02FZU2Y2 b_juncea 255 700 LYD501 b_juncea|10v2|E6ANDIZ02G70KP b_juncea 256 701 LYD514 soybean|11v1|GLYMA05G04990 soybean 257 702 LYD496 arabidopsis|10v1|AT1G58235 arabidopsis 258 — LYD289 arabidopsis|10v1|AT1G02040 arabidopsis 259 456 LYD290 arabidopsis|10v1|AT1G09560 arabidopsis 260 457 LYD291 arabidopsis|10v1|AT1G10970 arabidopsis 261 458 LYD292 arabidopsis|10v1|AT1G13740 arabidopsis 262 459 LYD293 arabidopsis|10v1|AT1G14620 arabidopsis 263 460 LYD294 arabidopsis|10v1|AT1G27300 arabidopsis 264 461 LYD295 arabidopsis|10v1|AT1G27900 arabidopsis 265 462 LYD296 arabidopsis|10v1|AT1G30820 arabidopsis 266 463 LYD298 arabidopsis|10v1|AT1G55910 arabidopsis 268 465 LYD299 arabidopsis|10v1|AT1G61600 arabidopsis 269 466 LYD300 arabidopsis|10v1|AT1G61790 arabidopsis 270 467 LYD301 arabidopsis|10v1|AT1G74790 arabidopsis 271 468 LYD302 arabidopsis|10v1|AT1G77060 arabidopsis 272 469 LYD303 arabidopsis|10v1|AT2G01710 arabidopsis 273 470 LYD304 arabidopsis|10v1|AT2G03810 arabidopsis 274 471 LYD305 arabidopsis|10v1|AT2G05220 arabidopsis 275 472 LYD307 arabidopsis|10v1|AT2G17990 arabidopsis 277 474 LYD309 arabidopsis|10v1|AT2G40020 arabidopsis 279 476 LYD311 arabidopsis|10v1|AT2G40510 arabidopsis 281 478 LYD312 arabidopsis|10v1|AT2G42770 arabidopsis 282 479 LYD313 arabidopsis|10v1|AT3G04620 arabidopsis 283 480 LYD316 arabidopsis|10v1|AT3G09030 arabidopsis 285 482 LYD318 arabidopsis|10v1|AT3G11900 arabidopsis 286 483 LYD319 arabidopsis|10v1|AT3G14070 arabidopsis 287 484 LYD320 arabidopsis|10v1|AT3G15810 arabidopsis 288 485 LYD321 arabidopsis|10v1|AT3G18750 arabidopsis 289 486 LYD322 arabidopsis|10v1|AT3G21190 arabidopsis 290 487 LYD323 arabidopsis|10v1|AT3G44280 arabidopsis 291 488 LYD324 arabidopsis|10v1|AT3G47860 arabidopsis 292 489 LYD325 arabidopsis|10v1|AT3G49390 arabidopsis 293 490 LYD326 arabidopsis|10v1|AT3G49490 arabidopsis 294 491 LYD327 arabidopsis|10v1|AT3G51895 arabidopsis 295 492 LYD328 arabidopsis|10v1|AT3G59210 arabidopsis 296 493 LYD329 arabidopsis|10v1|AT3G62270 arabidopsis 297 494 LYD330 arabidopsis|10v1|AT4G13070 arabidopsis 298 495 LYD331 arabidopsis|10v1|AT4G17440 arabidopsis 299 496 LYD332 arabidopsis|10v1|AT4G35110 arabidopsis 300 497 LYD334 arabidopsis|10v1|AT5G03870 arabidopsis 301 498 LYD335 arabidopsis|10v1|AT5G04140 arabidopsis 302 499 LYD337 arabidopsis|10v1|AT5G11740 arabidopsis 303 500 LYD338 arabidopsis|10v1|AT5G12410 arabidopsis 304 501 LYD339 arabidopsis|10v1|AT5G13560 arabidopsis 305 502 LYD340 arabidopsis|10v1|AT5G16420 arabidopsis 306 503 LYD341 arabidopsis|10v1|AT5G36700 arabidopsis 307 504 LYD342 arabidopsis|10v1|AT5G44680 arabidopsis 308 505 LYD343 arabidopsis|10v1|AT5G46150 arabidopsis 309 506 LYD344 arabidopsis|10v1|AT5G64840 arabidopsis 310 507 LYD346 b_juncea|10v2|BJ1SLX00003156 b_juncea 311 508 LYD355 b_juncea|10v2|E6ANDIZ01AM1M7 b_juncea 319 516 LYD362 b_juncea|10v2|E6ANDIZ01C68KB b_juncea 326 523 LYD368 b_juncea|10v2| b_juncea 331 528 OXBJ1SLX00002741D1T1 LYD372 canola|10v1|CD828626 canola 333 531 LYD376 canola|10v1|ES964015 canola 335 533 LYD380 cotton|10v1barbadense|BE054896 cotton 339 537 LYD395 medicago|09v1|AL379818 medicago 350 549 LYD399 medicago|09v1|AW688882 medicago 354 553 LYD401 medicago|09v1|AW690536 medicago 355 554 LYD402 medicago|09v1|AW694333 medicago 356 555 LYD407 medicago|09v1|BE322971 medicago 360 559 LYD414 medicago|09v1|BQ157221 medicago 365 564 LYD423 sorghum|09v1|SB01G027910 sorghum 373 573 LYD424 sorghum|09v1|SB01G046300 sorghum 374 574 LYD425 sorghum|09v1|SB02G004290 sorghum 375 575 LYD427 sorghum|09v1|SB03G025240 sorghum 376 576 LYD431 sorghum|09v1|SB05G020810 sorghum 378 578 LYD432 sorghum|09v1|SB06G021780 sorghum 379 579 LYD433 sorghum|09v1|SB07G014630 sorghum 380 580 LYD434 sorghum|09v1|SB07G019310 sorghum 381 581 LYD435 sorghum|09v1|SB07G019840 sorghum 382 582 LYD437 soybean|11v1|GLYMA01G09460 soybean 384 584 LYD438 soybean|11v1|GLYMA02G33320 soybean 385 585 LYD439 soybean|11v1|GLYMA03G34340 soybean 386 586 LYD440 soybean|11v1|GLYMA03G40870 soybean 387 587 LYD441 soybean|11v1|GLYMA04G36500 soybean 388 588 LYD442 soybean|11v1|GLYMA04G39480 soybean 389 589 LYD443 soybean|11v1|GLYMA04G41020 soybean 390 590 LYD445 soybean|11v1|GLYMA06G03510 soybean 391 591 LYD448 soybean|11v1|GLYMA07G08010 soybean 393 594 LYD450 soybean|11v1|GLYMA09G26770 soybean 395 596 LYD451 soybean|11v1|GLYMA09G29610 soybean 396 597 LYD453 soybean|11v1|GLYMA11G01120 soybean 398 599 LYD454 soybean|11v1|GLYMA11G03570 soybean 399 600 LYD458 soybean|11v1|GLYMA13G22110 soybean 402 603 LYD459 soybean|11v1|GLYMA13G23920 soybean 403 604 LYD460 soybean|11v1|GLYMA13G28620 soybean 404 605 LYD461 soybean|11v1|GLYMA15G37980 soybean 405 606 LYD465 soybean|11v1|GLYMA17G18250 soybean 407 608 LYD466 soybean|11v1|GLYMA18G49340 soybean 408 609 LYD467 soybean|11v1|GLYMA19G14700 soybean 409 610 LYD468 soybean|11v1|GLYMA19G36240 soybean 410 611 LYD469 soybean|11v1|GLYMA19G38830 soybean 411 612 LYD471 soybean|11v1|GLYMA20G38820 soybean 413 614 LYD472 soybean|gb168|AW348492 soybean 414 615 LYD473 soybean|gb168|BE661322 soybean 415 616 LYD474 sunflower|10v1|CD849185 sunflower 416 617 LYD475 tomato|09v1|AI485596 tomato 417 618 LYD477 tomato|09v1|BP884530 tomato 418 619 LYD478 tomato|10v1|AI483112 tomato 419 620 LYD479 tomato|10v1|AI484249 tomato 420 621 LYD481 tomato|10v1|AI771986 tomato 422 623 LYD482 tomato|10v1|AI777950 tomato 423 624 LYD484 tomato|10v1|AW929870 tomato 425 626 LYD489 tomato|10v1|BG131472 tomato 427 628 LYD491 tomato|10v1|BM061560 tomato 428 629 LYD492 tomato|10v1|DB714406 tomato 429 630 LYD495 wheat|gb164|BG604441 wheat 430 631 LYD498 b_juncea|10v2|E6ANDIZ01AJQJC b_juncea 432 633 LYD499 b_juncea|10v2|E6ANDIZ01B9PEA b_juncea 433 634 LYD500 b_juncea|10v2|E6ANDIZ02FZU2Y2 b_juncea 434 635 LYD503 maize|10v1|AI637036 maize 437 638 LYD504 medicago|09v1|AA660909 medicago 438 639 LYD506 medicago|09v1|BE239698 medicago 440 641 LYD507 sorghum|09v1|SB01G017330 sorghum 441 642 LYD508 sorghum|09v1|SB02G014460 sorghum 442 643 LYD509 sorghum|09v1|SB02G028300 sorghum 443 644 LYD510 sorghum|09v1|SB09G025320 sorghum 444 645 LYD511 soybean|11v1|BE660230 soybean 445 646 LYD512 soybean|11v1|GLYMA03G36420 soybean 446 647 LYD513 soybean|11v1|GLYMA03G39480 soybean 447 648 LYD514 soybean|11v1|GLYMA05G04990 soybean 448 649 LYD515 soybean|11v1|GLYMA07G36970 soybean 449 650 LYD516 soybean|11v1|GLYMA13G24040 soybean 450 651 LYD517 soybean|11v1|GLYMA15G06930 soybean 451 652 LYD519 soybean|gb168|AW686841 soybean 453 654 LYD297 arabidopsis|10v1|AT1G51440 arabidopsis 267 703 LYD306 arabidopsis|10v1|AT2G07674 arabidopsis 276 704 LYD308 arabidopsis|10v1|AT2G37478 arabidopsis 278 705 LYD310 arabidopsis|10v1|AT2G40300 arabidopsis 280 706 LYD315 arabidopsis|10v1|AT3G05390 arabidopsis 284 707 LYD347 b_juncea|10v2|BJ1SLX00219277D1 b_juncea 312 708 LYD348 b_juncea|10v2|BJ1SLX01241733D1 b_juncea 313 709 LYD349 b_juncea|10v2|E6ANDIZ01A0PVA b_juncea 314 710 LYD351 b_juncea|10v2|E6ANDIZ01A2WXZ b_juncea 315 711 LYD352 b_juncea|10v2|E6ANDIZ01A7124 b_juncea 316 712 LYD353 b_juncea|10v2|E6ANDIZ01AK44C b_juncea 317 713 LYD354 b_juncea|10v2|E6ANDIZ01ALST2 b_juncea 318 714 LYD356 b_juncea|10v2|E6ANDIZ01AR3Y3 b_juncea 320 715 LYD357 b_juncea|10v2|E6ANDIZ01AU0CH b_juncea 321 716 LYD358 b_juncea|10v2|E6ANDIZ01AUG5K b_juncea 322 717 LYD359 b_juncea|10v2|E6ANDIZ01AVIGM b_juncea 323 718 LYD360 b_juncea|10v2|E6ANDIZ01BHOKJ b_juncea 324 719 LYD361 b_juncea|10v2|E6ANDIZ01BIDFA b_juncea 325 720 LYD364 b_juncea|10v2|E6ANDIZ01ET44E b_juncea 327 721 LYD365 b_juncea|10v2|E6ANDIZ01EWUI0 b_juncea 328 722 LYD366 b_juncea|10v2|E6ANDIZ02FS13L b_juncea 329 723 LYD367 b_juncea|10v2|E6ANDIZ02GKPXS b_juncea 330 724 LYD370 barley|10v2|AV834829 barley 332 725 LYD375 canola|10v1|DY011663 canola 334 726 LYD377 canola|10v1|EV098360 canola 336 727 LYD378 canola|10v1|EV114958 canola 337 728 LYD379 canola|10v1|EV129887 canola 338 729 LYD382 cotton|10v2|AI726887 cotton 340 730 LYD383 cotton|10v2|BG447338 cotton 341 731 LYD385 cotton|10v2|DN799940 cotton 342 732 LYD386 cotton|10v2|DN804420 cotton 343 733 LYD387 cotton|10v2|DT466425 cotton 344 734 LYD388 cotton|10v2|EX167553 cotton 345 735 LYD390 cotton|gb164|AI055341 cotton 346 736 LYD391 maize|10v1|AA011869 maize 347 737 LYD392 maize|10v1|BE512624 maize 348 738 LYD393 medicago|09v1|AI974481 medicago 349 739 LYD396 medicago|09v1|AW256719 medicago 351 740 LYD397 medicago|09v1|AW257291 medicago 352 741 LYD398 medicago|09v1|AW329709 medicago 353 742 LYD403 medicago|09v1|AW698677 medicago 357 743 LYD404 medicago|09v1|AW736500 medicago 358 744 LYD405 medicago|09v1|AW775077 medicago 359 745 LYD408 medicago|09v1|BE324051 medicago 361 746 LYD409 medicago|09v1|BF521188 medicago 362 747 LYD410 medicago|09v1|BG452469 medicago 363 748 LYD413 medicago|09v1|BQ124797 medicago 364 749 LYD415 medicago|09v1|CX516971 medicago 366 750 LYD416 medicago|09v1|LLAJ388869 medicago 367 751 LYD417 medicago|09v1|LLAL373168 medicago 368 752 LYD418 medicago|09v1|LLAW688750 medicago 369 753 LYD419 medicago|09v1|LLAW698759 medicago 370 754 LYD420 medicago|09v1|LLAW776476 medicago 371 755 LYD422 medicago|09v1|MT454X026824 medicago 372 756 LYD428 sorghum|09v1|SB04G002930 sorghum 377 757 LYD436 sorghum|09v1|SB09G003870 sorghum 383 758 LYD446 soybean|11v1|GLYMA06G17910 soybean 392 759 LYD449 soybean|11v1|GLYMA07G10060 soybean 394 760 LYD452 soybean|11v1|GLYMA09G31720 soybean 397 761 LYD455 soybean|11v1|GLYMA11G11560 soybean 400 762 LYD456 soybean|11v1|GLYMA12G01770 soybean 401 763 LYD462 soybean|11v1|GLYMA16G04350 soybean 406 764 LYD470 soybean|11v1|GLYMA19G43610 soybean 412 765 LYD480 tomato|10v1|AI771275 tomato 421 766 LYD483 tomato|10v1|AW738746 tomato 424 767 LYD487 tomato|10v1|BG127385 tomato 426 768 LYD497 b_juncea|10v2|E6ANDIZ01AJCUK b_juncea 431 769 LYD501 b_juncea|10v2|E6ANDIZ02G70KP b_juncea 435 770 LYD502 cotton|10v2|DW503396 cotton 436 771 LYD505 medicago|09v1|AJ388789 medicago 439 772 LYD518 soybean|11v1|GLYMA18G48880 soybean 452 773 LYD520 soybean|gb168|FG994976 soybean 454 774 LYD496 arabidopsis|10v1|AT1G58235 arabidopsis 455 — Table 53: Provided are the identified genes, their annotation, organism and polynucleotide and polypeptide sequence identifiers. “polynucl.” = polynucleotide; “polypep.” = polypeptide.

Example 13 Identification of Homologous Sequences that Increase Seed Yield, Oil Yield, Growth Rate, Oil Content, Fiber Yield, Fiber Quality, Biomass, Vigor, ABST and/or NUE of a Plant

The concepts of orthology and paralogy have recently been applied to functional characterizations and classifications on the scale of whole-genome comparisons. Orthologs and paralogs constitute two major types of homologs: The first evolved from a common ancestor by specialization, and the latter are related by duplication events. It is assumed that paralogs arising from ancient duplication events are likely to have diverged in function while true orthologs are more likely to retain identical function over evolutionary time.

To identify putative orthologs of the genes affecting plant yield, oil yield, oil content, seed yield, growth rate, vigor, biomass, abiotic stress tolerance and/or nitrogen use efficiency, all sequences were aligned using the BLAST® (Basic Local Alignment Search Tool). Sequences sufficiently similar were tentatively grouped. These putative orthologs were further organized under a Phylogram—a branching diagram (tree) assumed to be a representation of the evolutionary relationships among the biological taxa. Putative ortholog groups were analyzed as to their agreement with the phylogram and in cases of disagreements these ortholog groups were broken accordingly.

Expression data was analyzed and the EST libraries were classified using a fixed vocabulary of custom terms such as developmental stages (e.g., genes showing similar expression profile through development with up regulation at specific stage, such as at the seed filling stage) and/or plant organ (e.g., genes showing similar expression profile across their organs with up regulation at specific organs such as seed). The annotations from all the ESTs clustered to a gene were analyzed statistically by comparing their frequency in the cluster versus their abundance in the database, allowing the construction of a numeric and graphic expression profile of that gene, which is termed “digital expression”. The rationale of using these two complementary methods with methods of phenotypic association studies of QTLs, SNPs and phenotype expression correlation is based on the assumption that true orthologs are likely to retain identical function over evolutionary time. These methods provide different sets of indications on function similarities between two homologous genes, similarities in the sequence level-identical amino acids in the protein domains and similarity in expression profiles.

The search and identification of homologous genes involves the screening of sequence information available, for example, in public databases such as the DNA Database of Japan (DDBJ), Genbank, and the European Molecular Biology Laboratory Nucleic Acid Sequence Database (EMBL) or versions thereof or the MIPS database. A number of different search algorithms have been developed, including but not limited to the suite of programs referred to as BLAST® programs. There are five implementations of BLAST®, three designed for nucleotide sequence queries (BLASTN, BLASTX, and TBLASTX) and two designed for protein sequence queries (BLASTP and TBLASTN) (Coulson, Trends in Biotechnology: 76-80, 1994; Birren et al., Genome Analysis, I: 543, 1997). Such methods involve alignment and comparison of sequences. The BLAST® algorithm calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences. The software for performing BLAST® analysis is publicly available through the National Centre for Biotechnology Information. Other such software or algorithms are GAP, BESTFIT, FASTA and TFASTA. GAP uses the algorithm of Needleman and Wunsch (J. Mol. Biol. 48: 443-453, 1970) to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps.

The homologous genes may belong to the same gene family. The analysis of a gene family may be carried out using sequence similarity analysis. To perform this analysis one may use standard programs for multiple alignments e.g. Clustal W. A neighbour-joining tree of the proteins homologous to the genes in this invention may be used to provide an overview of structural and ancestral relationships. Sequence identity may be calculated using an alignment program as described above. It is expected that other plants will carry a similar functional gene (ortholog) or a family of similar genes and those genes will provide the same preferred phenotype as the genes presented here. Advantageously, these family members may be useful in the methods of the invention. Example of other plants are included here but not limited to, barley (Hordeum vulgare), Arabidopsis (Arabidopsis thaliana), maize (Zea mays), cotton (Gossypium), Oilseed rape (Brassica napus), Rice (Oryza sativa), Sugar cane (Saccharum officinarum), Sorghum (Sorghum bicolor), Soybean (Glycine max), Sunflower (Helianthus annuus), Tomato (Lycopersicon esculentum), Wheat (Triticum aestivum).

The above-mentioned analyses for sequence homology can be carried out on a full-length sequence, but may also be based on a comparison of certain regions such as conserved domains. The identification of such domains, would also be well within the realm of the person skilled in the art and would involve, for example, a computer readable format of the nucleic acids of the present invention, the use of alignment software programs and the use of publicly available information on protein domains, conserved motifs and boxes. This information is available in the PRODOM (Hypertext Transfer Protocol://World Wide Web (dot) biochem (dot) ucl (dot) ac (dot) uk/bsm/dbbrowser/protocol/prodomqry (dot) html), PR (Hypertext Transfer Protocol://pir (dot) Georgetown (dot) edu/) or Pfam (Hypertext Transfer Protocol://World Wide Web (dot) sanger (dot) ac (dot) uk/Software/Pfam/) database. Sequence analysis programs designed for motif searching may be used for identification of fragments, regions and conserved domains as mentioned above. Preferred computer programs include, but are not limited to, MEME, SIGNALSCAN, and GENESCAN.

A person skilled in the art may use the homologous sequences provided herein to find similar sequences in other species and other organisms. Homologues of a protein encompass, peptides, oligopeptides, polypeptides, proteins and enzymes having amino acid substitutions, deletions and/or insertions relative to the unmodified protein in question and having similar biological and functional activity as the unmodified protein from which they are derived. To produce such homologues, amino acids of the protein may be replaced by other amino acids having similar properties (conservative changes, such as similar hydrophobicity, hydrophilicity, antigenicity, propensity to form or break a-helical structures or 3-sheet structures). Conservative substitution tables are well known in the art (see for example Creighton (1984) Proteins. W.H. Freeman and Company). Homologues of a nucleic acid encompass nucleic acids having nucleotide substitutions, deletions and/or insertions relative to the unmodified nucleic acid in question and having similar biological and functional activity as the unmodified nucleic acid from which they are derived.

Table 54, hereinbelow, lists a summary of orthologous and homologous sequences of the polynucleotide sequences and polypeptide sequences presented in Table 53 above, which were identified from the databases using the NCBI BLAST® software (e.g., using the Blastp and tBlastn algorithms) and needle (EMBOSS package) as being at least 80% homologous to the selected polynucleotides and polypeptides, and which are expected to increase plant yield, seed yield, oil yield, oil content, growth rate, fiber yield, fiber quality, biomass, vigor, ABST and/or NUE of a plant.

Lengthy table referenced here US20190119695A1-20190425-T00001 Please refer to the end of the specification for access instructions.

Example 14 Gene Cloning and Generation of Binary Vectors for Plant Expression

To validate their role in improving oil content, plant yield, seed yield, oil content, biomass, growth rate, fiber yield, fiber quality, ABST, NUE and/or vigor, selected genes were over-expressed in plants, as follows.

Cloning Strategy

Selected genes from those listed in Examples 12 and 13 hereinabove were cloned into binary vectors for the generation of transgenic plants. For cloning, the full-length open reading frame (ORF) was first identified. In case of ORF-EST clusters and in some cases already published mRNA sequences were analyzed to identify the entire open reading frame by comparing the results of several translation algorithms to known proteins from other plant species. To clone the full-length cDNAs, reverse transcription (RT) followed by polymerase chain reaction (PCR; RT-PCR) was performed on total RNA extracted from leaves, flowers, siliques or other plant tissues, growing under normal and different treated conditions. Total RNA was extracted as described in “GENERAL EXPERIMENTAL AND BIOINFORMATICS METHODS” above. Production of cDNA and PCR amplification was performed using standard protocols described elsewhere (Sambrook J., E. F. Fritsch, and T. Maniatis. 1989. Molecular Cloning. A Laboratory Manual., 2nd Ed. Cold Spring Harbor Laboratory Press, New York.) which are well known to those skilled in the art. PCR products are purified using PCR purification kit (Qiagen). In case where the entire coding sequence was not found, RACE kit from Invitrogen (RACE=R apid A mplification of cDNA E nds) was used to access the full cDNA transcript of the gene from the RNA samples described above. RACE products were cloned into high copy vector followed by sequencing or directly sequenced.

The information from the RACE procedure was used for cloning of the full length ORF of the corresponding genes.

In case genomic DNA is cloned, the genes were amplified by direct PCR on genomic DNA extracted from leaf tissue using the DNAeasy kit (Qiagen Cat. No. 69104).

Usually, 2 sets of primers were synthesized for the amplification of each gene from a cDNA or a genomic sequence; an external set of primers and an internal set (nested PCR primers). When needed (e.g., when the first PCR reaction does not result in a satisfactory product for sequencing), an additional primer (or two) of the nested PCR primers was used.

To facilitate cloning of the cDNAs/genomic sequences, a 8-12 bp extension was added to the 5′ of each primer. The primer extension includes an endonuclease restriction site. The restriction sites were selected using two parameters: (a). The site does not exist in the cDNA sequence; and (b). The restriction sites in the forward and reverse primers are designed such that the digested cDNA is inserted in the sense formation into the binary vector utilized for transformation.

Each digested PCR product was inserted into a high copy vector pUC19 (New England BioLabs Inc], or into plasmids originating from this vector. In some cases the undigested PCR product was inserted into pCR-Blunt II-TOPO (Invitrogen).

Sequencing of the amplified PCR products was performed, using ABI 377 sequencer (Amersham Biosciences Inc). In some cases, after confirming the sequences of the cloned genes, the cloned cDNA was introduced into a modified pGI binary vector containing the At6669 promoter via digestion with appropriate restriction endonucleases. In any case the insert was followed by single copy of the NOS terminator (SEQ ID NO: 14481). The digested products and the linearized plasmid vector were ligated using T4 DNA ligase enzyme (Roche, Switzerland).

High copy plasmids containing the cloned genes were digested with the restriction endonucleases (New England BioLabs Inc) according to the sites designed in the primers and cloned into binary vectors.

Several DNA sequences of the selected genes were synthesized by a commercial supplier GeneArt [Hypertext Transfer Protocol://World Wide Web (dot) geneart (dot) com/]. Synthetic DNA was designed in silico. Suitable restriction enzymes sites were added to the cloned sequences at the 5′ end and at the 3′ end to enable later cloning into the pQFNc binary vector downstream of the At6669 promoter (SEQ ID NO: 14467).

Binary vectors used for cloning: The plasmid pPI was constructed by inserting a synthetic poly-(A) signal sequence, originating from pGL3 basic plasmid vector (Promega, Acc No U47295; bp 4658-4811) into the Hindlll restriction site of the binary vector pBI101.3 (Clontech, Acc. No. U12640). pGI (pBXYN) is similar to pPI, but the original gene in the backbone, the GUS gene, is replaced by the GUS-Intron gene followed by the NOS terminator (SEQ ID NO: 14481) (Vancanneyt. G, et al MGG 220, 245-50, 1990). pGI was used in the past to clone the polynucleotide sequences, initially under the control of 35S promoter [Odell, J T, et al. Nature 313, 810-812 (28 Feb. 1985); SEQ ID NO: 14465].

The modified pGI vectors [pQXNc (FIG. 8); or pQFN (FIG. 2), pQFNc (FIG. 2) or pQYN 6669 (FIG. 1)] are modified versions of the pGI vector in which the cassette is inverted between the left and right borders so the gene and its corresponding promoter are close to the right border and the NPTII gene is close to the left border.

At6669, the Arabidopsis thaliana promoter sequence (SEQ ID NO:14467) was inserted in the modified pGI binary vector, upstream to the cloned genes, followed by DNA ligation and binary plasmid extraction from positive E. coli colonies, as described above.

Colonies were analyzed by PCR using the primers covering the insert which are designed to span the introduced promoter and gene. Positive plasmids were identified, isolated and sequenced.

Selected genes cloned by the present inventors are provided in Table 55 below.

TABLE 55 Genes cloned in High copy number plasmids Polyn. Polyp. SEQ ID SEQ ID Gene Name High copy plasmid Organism Primers used SEQ ID NOs: NO: NO: LYD289 pUC19c_LYD289 Arabidopsis thalia 14482, 14670, 14482, 14670 259 456 LYD290 pUC19c_LYD290 Arabidopsis thalia 14483, 14671 260 457 LYD291 pUC19c_LYD291 Arabidopsis thalia 14484, 14672 261 458 LYD292 pUC19c_LYD292 Arabidopsis thalia 14485, 14673, 14858, 14955 262 459 LYD293 pUC19c_LYD293 Arabidopsis thalia 14486, 14674, 14859, 14956 263 460 LYD294 pUC19c_LYD294 Arabidopsis thalia 14487, 14675, 14860, 14957 264 461 LYD295 pUC19c_LYD295 Arabidopsis thalia 14488, 14676, 14488, 14676 265 462 LYD296 pUC19c_LYD296 Arabidopsis thalia 14489, 14677, 14861, 14958 266 463 LYD297 pUC19c_LYD297 Arabidopsis thalia 14490, 14678, 14862, 14678 267 703 LYD298 pUC19c_LYD298 Arabidopsis thalia 14491, 14679, 14863, 14959 268 465 LYD299 pMA_LYD299_GA GeneArt 269 466 LYD300 pOA_LYD300_GA GeneArt 270 467 LYD301 pUC19d_LYD301 Arabidopsis thalia 14492, 14680, 14864, 14960 271 468 LYD302 pUC19c_LYD302 Arabidopsis thalia 14493, 14681, 14493, 14961 272 469 LYD303 pUC19c_LYD303 Arabidopsis thalia 14494, 14682, 14865, 14962 273 470 LYD304 pUC19c_LYD304 Arabidopsis thalia 14495, 14683, 14495, 14683 274 471 LYD305 pUC19c_LYD305 Arabidopsis thalia 14496, 14684, 14866, 14963 275 472 LYD306 pUC19c_LYD306 Arabidopsis thalia 14497, 14685 276 704 LYD307 pUC19c_LYD307 Arabidopsis thalia 14498, 14686, 14867, 14964 277 474 LYD308 pUC19c_LYD308 Arabidopsis thalia 14499, 14687, 14868, 14965 278 705 LYD309 pUC19c_LYD309 Arabidopsis thalia 14500, 14688, 14500, 14966 279 476 LYD310 pUC19c_LYD310 Arabidopsis thalia 14501, 14689, 14501, 14689 280 706 LYD311 pUC19c_LYD311 Arabidopsis thalia 14502, 14690, 14502, 14690 281 478 LYD312 pUC19c_LYD312 Arabidopsis thalia 14503, 14691, 14503, 14691 282 479 LYD313 pUC19c_LYD313 Arabidopsis thalia 14504, 14692, 14504, 14692 283 480 LYD315 pUC19c_LYD315 Arabidopsis thalia 14505, 14693, 14869, 14967 284 707 LYD316 pUC19c_LYD316 Arabidopsis thalia 14506, 14694, 14506, 14694 285 482 LYD318 pUC19c_LYD318 Arabidopsis thalia 14507, 14695, 14870, 14968 286 483 LYD319 pUC19c_LYD319 Arabidopsis thalia 14508, 14696, 14871, 14696 287 484 LYD320 pUC19c_LYD320 Arabidopsis thalia 14509, 14697, 14872, 14969 288 485 LYD321 pUC19c_LYD321 Arabidopsis thalia 14510, 14698, 14873, 14970 289 486 LYD322 pUC19c_LYD322 Arabidopsis thalia 14511, 14699, 14874, 14971 290 487 LYD323 pUC19c_LYD323 Arabidopsis thalia 14512, 14700, 14875, 14972 291 488 LYD324 pUC19c_LYD324 Arabidopsis thalia 14513, 14701 292 489 LYD325 pUC19c_LYD325 Arabidopsis thalia 14514, 14702, 14514, 14702 293 490 LYD326 pUC19c_LYD326 Arabidopsis thalia 14515, 14703 294 491 LYD327 TopoB_LYD327 Arabidopsis thalia 14516, 14704, 14877, 14974 295 492 LYD328 pUC19c_LYD328 Arabidopsis thalia 14517, 14705, 14878, 14975 296 493 LYD329 pUC19c_LYD329 Arabidopsis thalia 14518, 14706, 14879, 14976 297 494 LYD330 pUC19c_LYD330 Arabidopsis thalia 14519, 14707, 14880, 14977 298 495 LYD331 pUC19c_LYD331 Arabidopsis thalia 14520, 14708, 14881, 14978 299 496 LYD332 pUC19c_LYD332 Arabidopsis thalia 14521, 14709, 14882, 14979 300 497 LYD334 pUC19c_LYD334 Arabidopsis thalia 14522, 14710, 14522, 14980 301 498 LYD335 pUC19c_LYD335 Arabidopsis thalia 14523, 14711, 14883, 14981 302 499 LYD337 pUC19c_LYD337 Arabidopsis thalia 14524, 14712 303 500 LYD338 pUC19c_LYD338 Arabidopsis thalia 14525, 14713, 14525, 14982 304 501 LYD339 pUC19c_LYD339 Arabidopsis thalia 14526, 14714, 14884, 14983 305 502 LYD340 pUC19c_LYD340 Arabidopsis thalia 14527, 14715, 14527, 14715 306 503 LYD341 pUC19c_LYD341 Arabidopsis thalia 14528, 14716, 14885, 14984 307 504 LYD342 pUC19c_LYD342 Arabidopsis thalia 14529, 14717, 14886, 14985 308 505 LYD343 pUC19c_LYD343 Arabidopsis thalia 14530, 14718, 14887, 14986 309 506 LYD344 pUC19c_LYD344 Arabidopsis thalia 14531, 14719, 14531, 14719 310 507 LYD346 pUC19c_LYD346 Brassica juncea 14532, 14720, 14532, 14720 311 508 LYD347 pUC19c_LYD347 Brassica juncea 14533, 14721, 14888, 14721 312 708 LYD348 pUC19c_LYD348 Brassica juncea 14534, 14722, 14889, 14987 313 709 LYD349 pUC19c_LYD349 Brassica juncea 14535, 14723, 14535, 14723 314 710 LYD351 pUC19c_LYD351 Brassica juncea 14536, 14724, 14890, 14988 315 711 LYD352 pUC19_LYD352 Brassica juncea 14537, 14725, 14537, 14725 316 712 LYD353 pUC19c_LYD353 Brassica juncea 14538, 14726, 14538, 14726 317 713 LYD354 pUC19_LYD354 Brassica juncea 14539, 14727, 14539, 14727 318 714 LYD355 pUC19c_LYD355 Brassica juncea 14540, 14728, 14540, 14728 319 516 LYD356 pUC19c_LYD356 Brassica juncea 14541, 14729, 14541, 14729 320 715 LYD357 pUC19c_LYD357 Brassica juncea 14542, 14730, 14891, 14989 321 716 LYD358 pUC19_LYD358 Brassica juncea 14543, 14731, 14892, 14990 322 717 LYD359 pUC19c_LYD359 Brassica juncea 14544, 14732, 14544, 14991 323 718 LYD360 pUC19c_LYD360 Brassica juncea 14545, 14733, 14545, 14733 324 719 LYD361 pUC19c_LYD361 Brassica juncea 14546, 14734, 14546, 14734 325 720 LYD362 pUC19c_LYD362 Brassica juncea 14547, 14735, 14893, 14992 326 523 LYD364 pUC19_LYD364 Brassica juncea 14548, 14736, 14894, 14736 327 721 LYD365 pUC19c_LYD365 Brassica juncea 14549, 14737 328 722 LYD366 pUC19c_LYD366 Brassica juncea 14550, 14738, 14895, 14993 329 723 LYD367 pUC19c_LYD367 Brassica juncea 14551, 14739, 14551, 14739 330 724 LYD368 pUC19c_LYD368 Brassica juncea 14552, 14740, 14552, 14994 331 528 LYD370 pUC19c_LYD370 BARLEY Hordeum vulgare L. 14553, 14741, 14553, 14741 332 725 LYD372 pUC19d_LYD372 CANOLA Brassica napus 14554, 14742, 14896, 14995 333 531 LYD375 pUC19c_LYD375 CANOLA Brassica napus 14555, 14743, 14555, 14996 334 726 LYD376 pUC19c_LYD376 CANOLA Brassica napus 14556, 14744, 14897, 14997 335 533 LYD377 TopoB_LYD377 CANOLA Brassica napus 14557, 14745, 14898, 14998 336 727 LYD378 pUC19c_LYD378 CANOLA Brassica napus 14558, 14746, 14558, 14746 337 728 LYD379 pUC19c_LYD379 CANOLA Brassica napus 14559, 14747 338 729 LYD380 pMK-RQ_LYD380_GA GeneArt 339 537 LYD382 pUC19c_LYD382 COTTON Gossypium barbadense 14560, 14748, 14560, 14748 340 730 LYD383 pQFNc_LYD383 COTTON Gossypium hirsutum 14561, 14749, 14899, 14999 341 731 LYD385 pUC19c_LYD385 COTTON Gossypium barbadense 14562, 14750, 14900, 15000 342 732 LYD386 pUC19c_LYD386 COTTON Gossypium barbadense 14563, 14751, 14901, 15001 343 733 LYD387 pUC19c_LYD387 COTTON Gossypium barbadense 14564, 14752, 14902, 15002 344 734 LYD388 pUC19c_LYD388 COTTON Gossypium barbadense 14565, 14753, 14565, 14753 345 735 LYD390 pUC19c_LYD390 COTTON Gossypium barbadense 14566, 14754 346 736 LYD391 pUC19_LYD391 MAIZE Zea mays L. 14567, 14755, 14567, 14755 347 737 LYD392 pUC19c_LYD392 MAIZE Zea mays L. 14568, 14756, 14904, 15004 348 738 LYD393 pUC19c_LYD393 MEDICAGO Medicago trancatula 14569, 14757, 14569, 15005 349 739 LYD395 pUC19c_LYD395 MEDICAGO Medicago trancatula 14570, 14758, 14905, 15006 350 549 LYD396 pUC19c_LYD396 MEDICAGO Medicago trancatula 14571, 14759, 14906, 15007 351 740 LYD397 pUC19c_LYD397 MEDICAGO Medicago trancatula 14572, 14760, 14907, 15008 352 741 LYD398 pUC19c_LYD398 MEDICAGO Medicago trancatula 14573, 14761, 14573, 14761 353 742 LYD399 pUC19c_LYD399 MEDICAGO Medicago trancatula 14574, 14762, 14908, 15009 354 553 LYD401 pUC19c_LYD401 MEDICAGO Medicago trancatula 14575, 14763, 14909, 15010 355 554 LYD402 pUC19c_LYD402 MEDICAGO Medicago trancatula 14576, 14764, 14910, 15011 356 555 LYD403 pUC19c_LYD403 MEDICAGO Medicago trancatula 14577, 14765, 14911, 15012 357 743 LYD404 pUC19c_LYD404 MEDICAGO Medicago trancatula 14578, 14766, 14578, 15013 358 744 LYD405 pUC19c_LYD405 MEDICAGO Medicago trancatula 14579, 14767, 14579, 15014 359 745 LYD407 pMK-RQ_LYD407_GA GeneArt 360 559 LYD408 pUC19c_LYD408 MEDICAGO Medicago trancatula 14580, 14768, 14580, 15015 361 746 LYD409 pUC19c_LYD409 MEDICAGO Medicago trancatula 14581, 14769, 14912, 15016 362 747 LYD410 pUC19c_LYD410 MEDICAGO Medicago trancatula 14582, 14770, 14913, 15017 363 748 LYD413 pUC19d_LYD413 MEDICAGO Medicago trancatula 14583, 14771, 14914, 14771 364 749 LYD414 pUC19c_LYD414 MEDICAGO Medicago trancatula 14584, 14772, 14915, 15018 365 564 LYD415 pUC19c_LYD415 MEDICAGO Medicago trancatula 14585, 14773, 14916, 15019 366 750 LYD416 pUC19c_LYD416 MEDICAGO Medicago trancatula 14586, 14774, 14586, 14774 367 751 LYD417 pUC19c_LYD417 MEDICAGO Medicago trancatula 14587, 14775, 14587, 15020 368 752 LYD418 pUC19c_LYD418 MEDICAGO Medicago trancatula 14588, 14776, 14588, 14776 369 753 LYD419 pUC19c_LYD419 MEDICAGO Medicago trancatula 14589, 14777, 14917, 15021 370 754 LYD420 pUC19c_LYD420 MEDICAGO Medicago trancatula 14590, 14778, 14590, 14778 371 755 LYD422 pUC19c_LYD422 MEDICAGO Medicago trancatula 14591, 14779, 14918, 14779 372 756 LYD423 pUC19c_LYD423 Sorghum bicolor 14592, 14780, 14592, 15022 373 573 LYD424 pUC19c_LYD424 Sorghum bicolor 14593, 14781, 14593, 14781 374 574 LYD425 pUC19c_LYD425 Sorghum bicolor 14594, 14782, 14919, 15023 375 575 LYD427 pMA-RQ_LYD427_GA GeneArt 376 576 LYD428 pUC19c_LYD428 Sorghum bicolor 14595, 14783, 14595, 15024 377 757 LYD431 pMA_LYD431_GA GeneArt 378 578 LYD432 pUC19c_LYD432 Sorghum bicolor 14596, 14784, 14920, 15025 379 579 LYD433 TopoB_LYD433 Sorghum bicolor 14597, 14785, 14597, 14785 380 580 LYD434 pUC19c_LYD434 Sorghum bicolor 14598, 14786, 14598, 14786 381 581 LYD435 pUC19c_LYD435 Sorghum bicolor 14599, 14787 382 582 LYD436 pUC19c_LYD436 Sorghum bicolor 14600, 14788, 14600, 14788 383 758 LYD437 pUC19c_LYD437 SOYBEAN Glycine max 14601, 14789, 14921, 15026 384 584 LYD438 pUC19c_LYD438 SOYBEAN Glycine max 14602, 14790, 14922, 15027 385 585 LYD439 pUC19c_LYD439 SOYBEAN Glycine max 14603, 14791, 14923, 15028 386 586 LYD440 pUC19c_LYD440 SOYBEAN Glycine max 14604, 14792, 14604, 15029 387 587 LYD441 pUC19c_LYD441 SOYBEAN Glycine max 14605, 14793, 14924, 15030 388 588 LYD442 pUC19c_LYD442 SOYBEAN Glycine max 14606, 14794, 14606, 14794 389 589 LYD443 pMA-RQ_LYD443_GA GeneArt 390 590 LYD445 pUC19d_LYD445 SOYBEAN Glycine max 14607, 14795, 14607, 14795 391 591 LYD446 pUC19c_LYD446p SOYBEAN Glycine max 14608, 14796 392 759 LYD448 pUC19c_LYD448 SOYBEAN Glycine max 14609, 14797, 14609, 15031 393 594 LYD449 pUC19c_LYD449 SOYBEAN Glycine max 14610, 14798, 14610, 15032 394 760 LYD450 pUC19c_LYD450 SOYBEAN Glycine max 14611, 14799, 14925, 15033 395 596 LYD451 pUC19c_LYD451 SOYBEAN Glycine max 14612, 14800, 14612, 14800 396 597 LYD452 pUC19c_LYD452 SOYBEAN Glycine max 14613, 14801, 14613, 14801 397 761 LYD453 pUC19c_LYD453 SOYBEAN Glycine max 14614, 14802, 14926, 15034 398 599 LYD454 pUC19c_LYD454 SOYBEAN Glycine max 14615, 14803, 14615, 14803 399 600 LYD455 pUC19c_LYD455 SOYBEAN Glycine max 14616, 14804, 14616, 15035 400 762 LYD456 TopoB_LYD456 SOYBEAN Glycine max 14617, 14805, 14927, 15036 401 763 LYD458 pUC19c_LYD458 SOYBEAN Glycine max 14618, 14806, 14928, 14806 402 603 LYD459 pUC19c_LYD459 SOYBEAN Glycine max 14619, 14807, 14619, 14807 403 604 LYD460 pUC19c_LYD460 SOYBEAN Glycine max 14620, 14808, 14620, 14808 404 605 LYD461 pUC19c_LYD461 SOYBEAN Glycine max 14621, 14809, 14929, 15037 405 606 LYD462 pUC19c_LYD462 SOYBEAN Glycine max 14622, 14810, 14622, 15038 406 764 LYD465 pUC19c_LYD465 SOYBEAN Glycine max 14623, 14811, 14623, 14811 407 608 LYD466 pUC19c_LYD466 SOYBEAN Glycine max 14624, 14812, 14930, 15039 408 609 LYD467 pMA-RQ_LYD467_GA GeneArt 409 610 LYD468 pMA_LYD468_GA GeneArt 410 611 LYD469 pUC19c_LYD469 SOYBEAN Glycine max 14625, 14813, 14625, 14813 411 612 LYD470 pUC19c_LYD470 SOYBEAN Glycine max 14626, 14814, 14931, 15040 412 765 LYD471 pUC19c_LYD471 SOYBEAN Glycine max 14627, 14815, 14627, 15041 413 614 LYD472 pUC19c_LYD472 SOYBEAN Glycine max 14628, 14816 414 615 LYD473 pUC19c_LYD473 SOYBEAN Glycine max 14629, 14817, 14629, 15043 415 616 LYD474 pUC19c_LYD474 SUNFLOWER Helianthus annuus 14630, 14818, 14932, 15044 416 617 LYD475 pUC19c_LYD475 TOMATO Lycopersicum ND 14631, 14819, 14933, 15045 417 618 LYD477 pUC19_LYD477 TOMATO Lycopersicum ND 14632, 14820, 14934, 15046 418 619 LYD478 pUC19c_LYD478 TOMATO Lycopersicum ND 14633, 14821, 14935, 15047 419 620 LYD479 pUC19c_LYD479 TOMATO Lycopersicum ND 14634, 14822, 14936, 14822 420 621 LYD480 pUC19_LYD480 TOMATO Lycopersicum ND 14635, 14823, 14937, 15048 421 766 LYD481 pUC19c_LYD481 TOMATO Lycopersicum ND 14636, 14824 422 623 LYD482 pUC19c_LYD482 TOMATO Lycopersicum ND 14637, 14825, 14938, 15049 423 624 LYD483 pUC19c_LYD483 TOMATO Lycopersicum ND 14638, 14826, 14638, 14826 424 767 LYD484 pUC19c_LYD484 TOMATO Lycopersicum ND 14639, 14827, 14939, 15050 425 626 LYD487 pUC19c_LYD487 TOMATO Lycopersicum ND 14640, 14828, 14940, 15051 426 768 LYD489 pUC19c_LYD489 TOMATO Lycopersicum ND 14641, 14829, 14941, 15052 427 628 LYD491 pUC19c_LYD491 TOMATO Lycopersicum ND 14642, 14830, 14942, 14830 428 629 LYD492 pUC19c_LYD492 TOMATO Lycopersicum ND 14643, 14831, 14643, 15053 429 630 LYD495 pUC19c_LYD495 WHEAT Triticum aestivum L. 14644, 14832, 14943, 15054 430 631 LYD496 pUC19c_LYD496 Arabidopsis thalia 14669, 14857, 14669, 14857 455 — LYD497 pUC19c_LYD497 Brassica juncea 14645, 14833, 14944, 15055 431 769 LYD498 pUC19c_LYD498 Brassica juncea 14646, 14834, 14646, 14834 432 633 LYD499 pUC19c_LYD499 Brassica juncca 14647, 14835, 14647, 14835 433 634 LYD500 pUC19_LYD500 Brassica juncca 14648, 14836, 14648, 14836 434 635 LYD501 pUC19c_LYD501 Brassica juncca 14649, 14837, 14945, 15056 435 770 LYD502 pUC19c_LYD502 COTTON Gossypium barbadense 14650, 14838 436 771 LYD503 pUC19c_LYD503 MAIZE Zea mays L. 14651, 14839, 14946, 15057 437 638 LYD504 pUC19c_LYD504 MEDICAGO Medicago trancatula 14652, 14840, 14652, 15058 438 639 LYD505 pUC19c_LYD505 MEDICAGO Medicago trancatula 14653, 14841, 14653, 15059 439 772 LYD506 pUC19c_LYD506 MEDICAGO Medicago trancatula 14654, 14842, 14947, 15060 440 641 LYD507 pUC19c_LYD507 Sorghum bicolor 14655, 14843, 14948, 15061 441 642 LYD508 pUC19d_LYD508 Sorghum bicolor 14656, 14844, 14949, 15062 442 643 LYD509 pUC19c_LYD509 Sorghum bicolor 14657, 14845, 14657, 14845 443 644 LYD510 pUC19c_LYD510 Sorghum bicolor 14658, 14846, 14658, 15063 444 645 LYD511 pUC19c_LYD511 SOYBEAN Glycine max 14659, 14847, 14950, 15064 445 646 LYD512 pUC19c_LYD512 SOYBEAN Glycine max 14660, 14848 446 647 LYD513 pUC19c_LYD513 SOYBEAN Glycine max 14661, 14849 447 648 LYD514 TopoB_LYD514 SOYBEAN Glycine max 14662, 14850, 14951, 15065 448 649 LYD515 pUC19c_LYD515 SOYBEAN Glycine max 14663, 14851, 14952, 15066 449 650 LYD516 pUC19c_LYD516 SOYBEAN Glycine max 14664, 14852, 14953, 15067 450 651 LYD517 pUC19c_LYD517 SOYBEAN Glycine max 14665, 14853 451 652 LYD518 pUC19c_LYD518 SOYBEAN Glycine max 14666, 14854, 14666, 14854 452 773 LYD519 pUC19c_LYD519 SOYBEAN Glycine max 14667, 14855, 14954, 15068 453 654 LYD520 pUC19c_LYD520 SOYBEAN Glycine max 14668, 14856 454 774 Table 55. “Polyn.”—Polynucleotide; “Polyp.”—polypeptide. For cloning of each gene at least 2 primers were used: Forward (Fwd) or Reverse (Rev). In some cases, 4 primers were used: External forward (EF), External reverse (ER), nested forward (NF) or nested reverse (NR). The sequences of the primers used for cloning the genes are provided in the sequence listing.

Example 15 Production of Transgenic Arabidopsis Plants Expressing the Identified Polynucleotides of Some Embodiments of the Invention Experimental Methods

Production of agrobacterium tumefaciens cells harboring the binary vectors according to some embodiments of the invention—Each of the binary vectors described in Example 14 above were used to transform Agrobacterium cells. Two additional binary constructs, having only the At6669 or the 35S promoter or no additional promoter were used as negative controls.

The binary vectors were introduced to Agrobacterium tumefaciens GV301, or LB4404 competent cells (about 10⁹ cells/mL) by electroporation. The electroporation was performed using a MicroPulser electroporator (Biorad), 0.2 cm cuvettes (Biorad) and EC-2 electroporation program (Biorad). The treated cells were cultured in LB liquid medium at 28° C. for 3 hours, then plated over LB agar supplemented with gentamycin (50 mg/L; for Agrobacterium strains GV301) or streptomycin (300 mg/L; for Agrobacterium strain LB4404) and kanamycin (50 mg/L) at 28° C. for 48 hours. Abrobacterium colonies, which are developed on the selective media, were further analyzed by PCR using the primers designed to span the inserted sequence in the pPI plasmid. The resulting PCR products were isolated and sequenced to verify that the correct polynucleotide sequences of the invention were properly introduced to the Agrobacterium cells.

Preparation of Arabidopsis plants for transformation—Arabidopsis thaliana var Columbia (T₀ plants) were transformed according to the Floral Dip procedure [Clough S J, Bent A F. (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16(6): 735-43; and Desfeux C, Clough S J, Bent A F. (2000) Female reproductive tissues are the primary targets of Agrobacterium-mediated transformation by the Arabidopsis floral-dip method. Plant Physiol. 123(3): 895-904] with minor modifications. Briefly, Arabidopsis thaliana Columbia (Co10) T₀ plants were sown in 250 ml pots filled with wet peat-based growth mix. The pots were covered with aluminum foil and a plastic dome, kept at 4° C. for 3-4 days, then uncovered and incubated in a growth chamber at 18-24° C. under 16/8 hours light/dark cycles. The T₀ plants were ready for transformation six days before anthesis.

Preparation of the agrobacterium carrying the binary vectors to transformation into Arabidopsis plants—Single colonies of Agrobacterium carrying the binary vectors harboring the genes of some embodiments of the invention were cultured in LB medium supplemented with kanamycin (50 mg/L) and gentamycin (50 mg/L). The cultures were incubated at 28° C. for 48 hours under vigorous shaking and centrifuged at 4000 rpm for 5 minutes. The pellets comprising Agrobacterium cells were resuspended in a transformation medium which contains half-strength (2.15 g/L) Murashige-Skoog (Duchefa); 0.044 μM benzylamino purine (Sigma); 112 μg/L B5 Gambourg vitamins (Sigma); 5% sucrose; and 0.2 ml/L Silwet L-77 (OSI Specialists, CT) in double-distilled water, at pH of 5.7.

Transformation of Arabidopsis plants with the agrobacterium—Transformation of T₀ plants was performed by inverting each plant into an Agrobacterium suspension such that the above ground plant tissue is submerged for 3-5 seconds. Each inoculated T₀ plant was immediately placed in a plastic tray, then covered with clear plastic dome to maintain humidity and was kept in the dark at room temperature for 18 hours to facilitate infection and transformation. Transformed (transgenic) plants were then uncovered and transferred to a greenhouse for recovery and maturation. The transgenic T₀ plants were grown in the greenhouse for 3-5 weeks until siliques are brown and dry, then seeds were harvested from plants and kept at room temperature until sowing.

Generation of T1 and T2 transgenic plants—For generating T₁ and T₂ transgenic plants harboring the genes, seeds collected from transgenic T₀ plants were surface-sterilized by soaking in 70% ethanol for 1 minute, followed by soaking in 5% sodium hypochlorite and 0.05% triton for 5 minutes. The surface-sterilized seeds were thoroughly washed in sterile distilled water then placed on culture plates containing half-strength Murashig-Skoog (Duchefa); 2% sucrose; 0.8% plant agar; 50 mM kanamycin; and 200 mM carbenicylin (Duchefa). The culture plates were incubated at 4° C. for 48 hours then transferred to a growth room at 25° C. for an additional week of incubation. Vital T₁ Arabidopsis plants were transferred to a fresh culture plates for another week of incubation. Following incubation the T₁ plants were removed from culture plates and planted in growth mix contained in 250 ml pots. The transgenic plants were allowed to grow in a greenhouse to maturity. Seeds harvested from T₁ plants were cultured and grown to maturity as T₂ plants under the same conditions as used for culturing and growing the T₁ plants.

Example 16 Evaluation of Transgenic Arabidopsis for Seed Yield and Plant Growth Rate Under Normal Conditions in Greenhouse Assays (GH-SM Assays)

Assay 1: Seed yield plant biomass and plant growth rate under normal greenhouse conditions—This assay follows seed yield production, the biomass formation and the rosette area growth of plants grown in the greenhouse at non-limiting nitrogen growth conditions. Transgenic Arabidopsis seeds were sown in agar media supplemented with ½ MS medium and a selection agent (Kanamycin). The T₂ transgenic seedlings were then transplanted to 1.7 trays filled with peat and perlite in a 1:1 ratio. The trays were irrigated with a solution containing 6 mM inorganic nitrogen in the form of KNO₃ with 1 mM KH₂PO₄, 1 mM MgSO₄, 2 mM CaCl₂ and microelements. All plants were grown in the greenhouse until mature seeds. Seeds were harvested, extracted and weight. The remaining plant biomass (the above ground tissue) was also harvested, and weighted immediately or following drying in oven at 50° C. for 24 hours.

Each construct was validated at its T₂ generation. Transgenic plants transformed with a construct conformed by an empty vector carrying the At6669 promoter and the selectable marker was used as control.

The plants were analyzed for their overall size, growth rate, flowering, seed yield, 1,000-seed weight, dry matter and harvest index (HI-seed yield/dry matter). Transgenic plants performance was compared to control plants grown in parallel under the same conditions. Mock-transgenic plants expressing the uidA reporter gene (GUS-Intron) or with no gene at all, under the same promoter were used as control.

The experiment was planned in nested randomized plot distribution. For each gene of the invention three to five independent transformation events were analyzed from each construct.

Digital imaging—A laboratory image acquisition system, which consists of a digital reflex camera (Canon EOS 300D) attached with a 55 mm focal length lens (Canon EF-S series), mounted on a reproduction device (Kaiser RS), which includes 4 light units (4×150 Watts light bulb) was used for capturing images of plant samples.

The image capturing process was repeated every 2 days starting from day 1 after transplanting till day 15. Same camera, placed in a custom made iron mount, was used for capturing images of larger plants sawn in white tubs in an environmental controlled greenhouse. The tubs are square shape include 1.7 liter trays. During the capture process, the tubs were placed beneath the iron mount, while avoiding direct sun light and casting of shadows.

An image analysis system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.39 [Java based image processing program which was developed at the U.S. National Institutes of Health and freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Images were captured in resolution of 10 Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute).

Leaf analysis—Using the digital analysis leaves data was calculated, including leaf number, rosette area, rosette diameter, and leaf blade area.

Vegetative growth rate: the relative growth rate (RGR) of leaf number [formula IX (described above)], rosette area [formula VIII (described above)], plot coverage (formula XIII, below) and harvest index [formula IV (described above)] was calculated with the indicated formulas.

Relative growth rate of plot coverage=Regression coefficient of plot coverage along time course.  Formula XIII

Seeds average weight—At the end of the experiment all seeds were collected. The seeds were scattered on a glass tray and a picture was taken. Using the digital analysis, the number of seeds in each sample was calculated.

Dry weight and seed yield—On about day 80 from sowing, the plants were harvested and left to dry at 30° C. in a drying chamber. The biomass and seed weight of each plot were measured and divided by the number of plants in each plot. Dry weight=total weight of the vegetative portion above ground (excluding roots) after drying at 30° C. in a drying chamber; Seed yield per plant=total seed weight per plant (gr). 1000 seed weight (the weight of 1000 seeds) (gr.).

The harvest index (HI) was calculated using Formula IV as described above.

Oil percentage in seeds—At the end of the experiment all seeds from each plot were collected. Seeds from 3 plots were mixed grounded and then mounted onto the extraction chamber. 210 ml of n-Hexane (Cat No. 080951 Biolab Ltd.) were used as the solvent. The extraction was performed for 30 hours at medium heat 50° C. Once the extraction has ended the n-Hexane was evaporated using the evaporator at 35° C. and vacuum conditions. The process was repeated twice. The information gained from the Soxhlet extractor (Soxhlet, F. Die gewichtsanalytische Bestimmung des Milchfettes, Polytechnisches J. (Dingler's) 1879, 232, 461) was used to create a calibration curve for the Low Resonance NMR. The content of oil of all seed samples was determined using the Low Resonance NMR (MARAN Ultra-Oxford Instrument) and its MultiQuant software package.

Silique length analysis—On day 50 from sowing, 30 siliques from different plants in each plot were sampled in block A. The chosen siliques were green-yellow in color and were collected from the bottom parts of a grown plant's stem. A digital photograph was taken to determine silique's length.

Statistical analyses—To identify outperforming genes and constructs, results from the independent transformation events tested were analyzed separately. Data was analyzed using Student's t-test and results are considered significant if the p value was less than 0.1. The JMP statistics software package was used (Version 5.2.1, SAS Institute Inc., Cary, N.C., USA).

Tables 56-60 summarize the observed phenotypes of transgenic plants exogenously expressing the gene constructs using the seed maturation (GH-SM) assays under normal conditions. The evaluation of each gene was performed by testing the performance of different number of events. Event with p-value<0.1 was considered statistically significant.

TABLE 56 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter Inflorescence Gene Dry Weight [mg] Flowering Emergence Name Event # Ave. P-Val. % Incr. Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD513 67217.3 — — — 38.5 0.02 −3 32.1 0.28 −1 LYD512 67209.1 — — — 38.6 0.13 −2 32.0 0.15 −1 LYD512 67209.4 — — — — — — 32.1 0.28 −1 LYD512 67211.1 — — — — — — 32.1 0.28 −1 LYD512 67212.2 — — — — — — 32.1 0.28 −1 LYD482 67334.1 — — — — — — 32.1 0.28 −1 LYD482 67334.3 — — — — — — 32.0 0.15 −1 LYD475 67202.3 — — — 38.8 0.07 −2 — — — LYD475 67204.4 — — — 38.0 0.02 −4 32.0 0.15 −1 LYD472 67332.1 — — — 37.6 L −5 32.0 0.15 −1 LYD472 67332.3 — — — 38.7 0.04 −2 32.0 0.15 −1 LYD472 67332.4 — — — 38.0 0.02 −4 32.0 0.15 −1 LYD466 67119.4 — — — — — — 32.1 0.28 −1 LYD466 67121.1 — — — 37.5 L −5 32.0 0.15 −1 LYD466 67121.3 — — — — — — 32.1 0.28 −1 LYD452 67106.2 — — — — — — 32.0 0.15 −1 LYD451 67187.7 — — — — — — 32.1 0.28 −1 LYD451 67188.1 — — — 38.9 0.11 −1 32.1 0.28 −1 LYD451 67188.4 — — — 38.3 0.26 −3 — — — LYD445 67353.1 — — — — — — 32.0 0.15 −1 LYD445 67353.2 — — — 38.5 0.02 −3 32.0 0.15 −1 LYD439 67095.6 — — — 39.0 0.20 −1 32.1 0.28 −1 LYD415 67264.5 — — — 38.8 0.07 −2 — — — LYD415 67266.1 — — — 39.0 0.20 −1 32.1 0.28 −1 LYD382 67175.2 — — — — — — 32.1 0.28 −1 LYD382 67176.3 — — — — — — 32.0 0.15 −1 LYD339 67246.3 — — — — — — 32.0 0.15 −1 LYD339 67247.6 — — — — — — 32.0 0.15 −1 LYD324 67167.1 — — — 38.7 0.08 −2 32.0 0.15 −1 LYD321 67280.1 — — — — — — 32.1 0.28 −1 LYD321 67283.1 — — — — — — 32.1 0.28 −1 LYD321 67283.4 — — — 38.0 0.02 −4 32.0 0.15 −1 LYD302 67413.1 — — — — — — 32.1 0.28 −1 LYD302 67414.2 — — — — — — 32.1 0.28 −1 LYD302 67416.3 — — — 38.7 0.04 −2 32.0 0.15 −1 LYD296 67358.6 — — — 38.8 0.08 −2 32.1 0.28 −1 LYD296 67360.1 — — — 38.7 0.09 −2 — — — LYD290 67233.1 — — — 39.0 0.20 −1 32.1 0.28 −1 LYD290 67233.5 — — — 38.6 0.03 −2 — — — CONT. — — — — 39.5 — — 32.3 — — LYD517 67222.1 — — — 37.5 0.05 −3 32.0 0.23 −1 LYD515 67151.1 — — — 37.1 0.18 −4 32.0 0.23 −1 LYD502 67341.5 — — — 37.5 0.05 −3 32.0 0.23 −1 LYD502 67342.2 — — — — — — 32.0 0.23 −1 LYD498 67252.3 — — — — — — 32.0 0.23 −1 LYD492 67364.1 — — — — — — 32.0 0.23 −1 LYD492 67366.3 — — — 37.1 0.06 −4 — — — LYD474 67199.1 — — — 37.7 0.10 −2 32.0 0.23 −1 LYD454 67192.5 — — — 37.6 0.07 −3 — — — LYD450 67178.4 — — — 37.6 0.07 −3 — — — LYD450 67182.2 — — — 37.6 0.07 −3 32.0 0.23 −1 LYD397 67322.1 — — — 37.6 0.07 −3 32.0 0.23 −1 LYD397 67324.2 — — — 37.1 0.06 −4 32.0 0.23 −1 LYD328 67238.2 — — — 37.1 0.06 −4 32.0 0.23 −1 LYD323 67286.4 — — — — — — 32.0 0.23 −1 LYD323 67287.1 — — — 37.0 0.12 −4 32.0 0.23 −1 LYD323 67287.3 — — — 36.8 0.01 −5 32.0 0.23 −1 LYD312 67256.4 — — — 37.5 0.05 −3 32.0 0.23 −1 LYD312 67256.5 — — — 37.6 0.07 −3 32.0 0.23 −1 LYD312 67257.1 — — — 37.9 0.29 −2 32.0 0.23 −1 LYD312 67257.3 — — — 37.5 0.05 −3 32.0 0.23 −1 LYD310 67160.2 — — — 38.0 0.29 −1 32.0 0.23 −1 LYD301 67347.1 — — — 37.9 0.29 −2 32.0 0.23 −1 LYD301 67347.2 — — — 37.1 0.06 −4 32.0 0.23 −1 LYD298 66962.3 — — — 37.9 0.29 −2 32.0 0.23 −1 LYD298 66964.4 — — — 37.5 0.05 −3 32.0 0.23 −1 LYD298 66966.1 — — — 37.6 0.07 −3 — — — LYD291 67402.2 — — — — — — 32.0 0.23 −1 CONT. — — — — 38.6 — — 32.4 — — LYD508 67823.2 1170.6 0.04 9 — — — — — — LYD508 67824.3 1310.0 0.22 22 37.9 0.08 −4 31.8 0.13 −2 LYD495 67731.2 1120.0 0.26 5 — — — — — — LYD495 67732.5 1178.1 0.23 10 — — — — — — LYD491 67874.3 1120.0 0.26 5 — — — — — — LYD491 67874.6 1187.5 0.03 11 — — — — — — LYD489 67784.4 1118.8 0.29 4 — — — — — — LYD479 67727.4 1198.8 0.02 12 — — — — — — LYD433 67702.4 1228.8 L 15 — — — — — — LYD428 67472.2 — — — 38.5 0.22 −3 32.0 0.20 −1 LYD428 67473.3 1204.4 0.17 12 37.6 0.14 −5 31.6 0.22 −3 LYD305 67533.1 1353.1 L 26 — — — — — — CONT. — 1071.0 — — 39.6 — — 32.5 — — LYD484 67133.3 — — — — — — 27.8 0.03 −4 LYD484 67135.3 — — — 34.8 0.08 −2 27.8 0.02 −4 LYD470 67125.4 — — — 34.5 0.02 −3 27.9 0.02 −4 LYD470 67126.7 — — — 33.8 0.28 −5 27.0 0.27 −7 LYD459 67112.1 — — — — — — 27.4 0.24 −6 LYD414 67091.1 — — — 33.8 0.28 −5 — — — LYD414 67091.2 — — — 33.7 0.16 −5 28.3 0.19 −2 LYD387 67316.1 — — — 34.7 0.17 −2 — — — LYD387 67317.1 — — — — — — 28.0 0.03 −3 LYD387 67317.4 — — — — — — 27.9 0.03 −4 LYD386 67860.3 — — — — — — 28.1 0.04 −3 LYD347 67848.2 — — — 34.5 0.02 −3 27.2 0.13 −6 LYD341 67055.2 — — — 34.8 0.08 −2 27.3 0.20 −6 LYD338 67442.3 — — — 33.9 0.26 −4 28.0 0.03 −3 LYD338 67443.1 — — — 34.7 0.17 −2 — — — LYD337 66994.3 — — — 34.3 L −3 — — — LYD337 66995.4 — — — 33.8 0.28 −5 27.3 0.20 −6 LYD322 66884.2 — — — 33.8 0.28 −5 27.5 0.13 −5 LYD322 66886.6 — — — 34.5 0.02 −3 — — — LYD322 66887.1 — — — 33.1 L −7 — — — LYD307 66977.3 — — — — — — 27.4 0.24 −6 CONT. — — — — 35.5 — — 29.0 — — LYD496 67737.2 — — — — — — 31.5 0.18 −2 LYD496 67739.1 — — — 37.1 0.11 −3 — — — LYD496 67741.6 — — — — — — 31.2 0.06 −2 LYD410 67546.3 1274.9 0.18 12 — — — 31.1 0.04 −3 LYD409 67468.2 1203.1 0.05 6 — — — — — — LYD405 67696.2 — — — — — — 31.6 0.28 −1 LYD403 67769.4 1375.0 L 21 — — — — — — LYD403 67771.1 — — — — — — 31.4 0.18 −2 LYD402 67760.2 1203.1 0.14 6 37.1 0.29 −3 — — — LYD379 67677.1 1181.9 0.14 4 — — — — — — LYD379 67678.1 — — — — — — 31.5 0.18 −2 LYD372 67673.4 1281.2 0.23 13 37.1 0.11 −3 31.2 0.06 −2 LYD366 67812.5 1192.5 0.08 5 — — — — — — LYD362 67538.2 1175.0 0.20 3 — — — — — — LYD362 67543.5 — — — 36.7 0.02 −4 31.3 0.21 −2 LYD355 67641.2 1180.0 0.15 4 — — — — — — LYD347 67844.2 1213.8 0.03 7 — — — 31.3 0.21 −2 LYD335 67557.5 — — — — — — 31.5 0.18 −2 CONT. — 1135.6 — — 38.1 — — 32.0 — — LYD504 67136.3 — — — 33.0 L −8 26.8 L −8 LYD504 67138.1 — — — 34.7 0.04 −3 27.9 0.02 −5 LYD504 67139.1 — — — — — — 27.6 0.16 −6 LYD504 67140.1 — — — 34.6 0.08 −3 — — — LYD466 67119.4 — — — 34.0 L −5 28.1 L −4 LYD442 67103.1 — — — — — — 28.0 L −4 LYD442 67104.3 — — — 34.7 0.06 −3 28.1 0.01 −4 LYD440 66902.1 — — — — — — 28.4 0.28 −3 LYD440 66903.1 — — — 34.7 0.06 −3 27.8 L −5 LYD425 67454.5 — — — 35.1 0.17 −2 28.1 L −4 LYD408 67304.1 — — — 34.4 0.02 −4 — — — LYD408 67305.6 — — — 34.7 0.11 −3 27.9 L −5 LYD408 67306.2 — — — 34.1 0.01 −5 28.0 L −4 LYD401 67086.3 — — — 34.9 0.09 −2 — — — LYD375 67071.4 — — — 34.9 0.18 −2 — — — LYD375 67073.2 — — — 34.4 0.02 −4 28.0 L −4 LYD342 67062.1 — — — 34.9 0.09 −2 28.4 0.28 −3 LYD329 67277.4 — — — 34.4 0.16 −4 28.0 L −4 LYD320 67040.3 — — — 34.8 0.09 −3 28.4 0.28 −3 LYD318 66980.5 — — — 35.0 0.16 −2 — — — LYD318 66982.1 — — — 34.9 0.19 −2 — — — LYD318 66983.4 — — — 33.4 0.03 −6 27.3 0.18 −7 LYD316 67436.1 — — — 34.7 0.06 −3 — — — LYD316 67439.1 — — — 34.7 0.06 −3 — — — LYD298 66962.3 — — — 35.1 0.17 −2 — — — LYD292 66998.3 — — — 34.5 0.03 −3 27.5 L −6 LYD292 66999.4 — — — 34.4 0.16 −4 28.4 0.25 −3 LYD292 67000.1 — — — 34.4 0.02 −4 28.9 0.28 −1 CONT. — — — — 35.8 — — 29.2 — — Table 56. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “P-val.”—p-value, L—p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 14467). “—” = results are still unavailable.

TABLE 57 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter Leaf Blade Area Plot Coverage Gene [cm²] Leaf Number [cm²] Name Event # Ave. P-Val. % Incr. Ave. P-Val. % Incr. Ave. VP-al. % Incr. LYD499 68152.2 1.1 0.22 1 — — — — — — LYD446 68110.1 1.1 0.14 15 — — — 63.1 0.03 18 LYD443 68163.1 1.1 0.05 15 — — — 62.3 0.14 17 LYD443 68164.1 1.0 0.06 4 — — — — — — LYD443 68164.2 1.2 L 18 — — — 64.2 0.12 20 LYD443 68165.3 1.1 L 12 9.8 0.25 3 62.8 L 18 LYD436 68073.3 1.1 0.09 15 10.1 0.05 5 64.4 0.02 21 LYD416 67904.3 1.0 0.21 4 — — — 56.4 0.03 6 LYD416 67907.6 1.0 0.19 6 — — — — — — LYD391 68156.4 1.0 0.15 5 — — — 58.0 L 9 LYD391 68160.4 1.2 L 22 — — — 68.4 0.09 28 LYD388 68096.2 1.2 L 19 — — — 63.4 L 19 LYD388 68098.2 1.2 0.04 25 — — — 69.1 L 29 LYD388 68098.3 1.1 L 14 — — — 57.9 0.14 9 LYD367 68066.5 1.2 0.01 25 — — — 68.7 0.14 29 LYD364 68018.4 1.1 0.17 12 — — — 60.2 0.03 13 LYD364 68020.1 1.1 0.07 8 — — — 55.3 0.29 3 LYD364 68020.5 1.3 0.05 26 9.9 0.22 3 72.5 L 36 LYD364 68022.1 1.1 0.14 14 — — — 62.5 0.15 17 LYD361 68147.1 1.0 0.12 4 — — — 56.2 0.25 5 LYD360 68061.1 1.2 0.11 19 — — — 65.1 0.02 22 LYD360 68063.2 1.1 0.04 12 — — — 58.2 0.26 9 LYD357 68228.1 1.1 L 9 — — — 57.8 0.20 8 LYD354 68133.4 1.1 0.12 12 — — — 61.7 0.11 16 LYD354 68133.6 1.1 0.14 8 — — — — — — LYD349 68085.5 1.4 0.11 38 9.8 0.25 3 76.9 0.08 44 LYD308 66881.2 1.1 0.25 14 9.9 0.22 3 63.2 0.02 18 LYD295 67972.2 — — — 10.0 0.07 5 63.3 0.17 18 LYD295 67972.4 — — — — — — 61.8 0.20 16 CONT. — 1.0 — — 9.6 — — 53.4 — — LYD513 67217.3 0.9 L 19 — — — 49.3 L 22 LYD512 67209.1 0.8 0.27 11 — — — — — — LYD482 67334.1 0.8 0.26 11 — — — — — — LYD482 67336.1 0.8 0.19 8 — — — — — — LYD475 67204.4 0.8 L 13 — — — 47.9 L 18 LYD472 67332.1 0.9 0.09 19 — — — 49.7 0.06 23 LYD472 67332.4 0.9 L 23 — — — 49.9 L 23 LYD466 67121.1 0.9 L 17 — — — 49.0 L 21 LYD452 67106.2 0.8 0.20 5 — — — 43.4 0.20 7 LYD451 67187.9 0.8 0.10 6 — — — 43.8 0.09 8 LYD451 67188.1 0.8 0.30 10 — — — — — — LYD451 67188.4 0.8 0.14 13 — — — 47.5 0.07 17 LYD445 67352.3 — — — 9.8 0.27 2 — — — LYD445 67353.1 0.8 0.20 7 — — — 43.5 0.27 7 LYD445 67353.2 0.8 L 12 — — — 46.8 L 16 LYD445 67354.5 — — — — — — 42.7 0.29 6 LYD439 67094.1 0.8 0.17 12 — — — — — — LYD439 67094.3 0.8 0.29 10 — — — 47.2 0.06 17 LYD439 67095.6 0.8 L 12 — — — 45.9 0.02 13 LYD415 67262.1 0.8 0.07 9 — — — 44.7 0.21 11 LYD415 67264.5 — — — — — — 43.5 0.13 7 LYD415 67266.6 0.8 0.28 7 — — — — — — LYD382 67174.1 0.8 0.30 15 — — — 45.8 0.19 13 LYD382 67175.2 0.9 0.10 16 — — — 47.4 0.16 17 LYD339 67247.3 0.8 0.11 6 — — — — — — LYD324 67167.1 — — — 9.8 0.17 2 — — — LYD321 67280.1 — — — 9.9 0.07 3 — — — LYD321 67283.1 0.8 L 14 — — — 47.8 0.01 18 LYD321 67283.3 0.8 0.16 9 — — — — — — LYD321 67283.4 1.0 0.10 34 — — — 55.2 0.04 36 LYD302 67414.3 0.9 L 16 — — — 46.2 0.03 14 LYD302 67416.3 0.8 0.03 13 — — — 45.5 0.02 12 LYD296 67358.6 0.9 0.24 21 — — — 50.1 0.14 24 LYD296 67360.4 — — — 9.8 0.17 2 — — — LYD290 67233.3 0.8 0.26 4 — — — — — — CONT. — 0.7 — — 9.6 — — 40.5 — — LYD517 67221.3 — — — — — — 30.1 0.14 6 LYD517 67222.1 0.6 0.22 14 — — — — — — LYD515 67151.1 0.6 0.01 18 — — — 33.3 0.08 17 LYD515 67152.4 0.7 L 26 — — — 36.7 L 29 LYD502 67340.4 0.6 0.19 9 — — — 31.9 0.09 13 LYD502 67341.5 0.6 0.04 15 9.6 0.07 5 32.6 0.04 15 LYD502 67342.1 — — — 9.4 0.16 2 — — — LYD502 67342.6 0.6 0.14 9 — — — 31.5 0.02 11 LYD498 67252.3 0.6 0.04 15 9.4 0.16 2 33.3 L 17 LYD498 67254.1 0.6 0.06 14 — — — 31.2 0.06 10 LYD498 67254.3 0.6 0.03 15 — — — 32.9 0.01 16 LYD492 67364.5 0.6 0.24 13 — — — 31.6 0.20 11 LYD474 67196.1 0.6 0.26 12 — — — — — — LYD474 67199.1 0.6 0.23 10 9.5 0.15 4 30.8 0.05 9 LYD454 67192.5 0.6 0.04 19 — — — 33.5 0.02 18 LYD450 67178.3 0.6 0.10 13 9.9 0.16 8 32.5 0.02 14 LYD450 67180.2 — — — — — — 31.6 0.27 11 LYD450 67182.2 0.6 0.01 18 9.6 0.03 4 33.5 0.01 18 LYD428 67474.4 — — — 9.6 0.22 4 — — — LYD397 67322.1 — — — — — — 30.1 0.28 6 LYD397 67324.2 0.7 L 29 — — — 36.3 0.04 28 LYD323 67286.1 0.6 0.19 13 — — — 33.0 0.29 16 LYD323 67287.3 0.6 0.04 15 — — — 32.8 L 16 LYD312 67256.4 0.7 0.06 28 9.8 0.04 6 37.0 0.08 30 LYD312 67256.5 0.6 0.03 15 — — — 32.9 L 16 LYD310 67161.1 0.6 0.22 8 — — — 31.7 0.04 12 LYD310 67164.1 — — — — — — 30.5 0.08 7 LYD301 67347.2 0.7 0.05 28 — — — 35.5 0.01 25 LYD301 67347.4 0.6 0.10 12 9.6 0.03 4 31.7 0.13 12 LYD298 66964.4 0.6 0.02 21 9.4 0.16 2 35.3 0.15 24 LYD298 66966.2 0.6 0.06 12 — — — 32.7 L 15 LYD291 67400.2 — — — 9.6 0.22 4 — — — LYD291 67402.2 0.6 0.14 11 — — — — — — CONT. — 0.5 — — 9.2 — — 28.4 — — LYD508 67823.1 — — — 9.9 0.26 4 — — — LYD508 67823.2 0.8 0.15 8 — — — 44.8 0.13 7 LYD508 67824.3 0.9 L 16 10.2 0.10 6 49.5 0.08 18 LYD503 67527.1 — — — 10.2 0.01 6 — — — LYD501 67887.3 — — — 10.1 0.21 6 — — — LYD497 67880.3 — — — 10.2 0.10 6 — — — LYD497 67881.4 — — — 9.8 0.23 2 — — — LYD497 67883.2 — — — 10.0 0.05 4 — — — LYD497 67883.4 0.8 0.03 9 — — — 46.0 0.03 10 LYD479 67727.4 0.9 0.08 20 10.1 0.05 6 53.6 0.21 28 LYD448 67917.2 — — — 9.9 0.22 3 — — — LYD441 67715.4 — — — 9.9 0.22 3 — — — LYD428 67473.3 0.9 L 21 10.3 0.21 8 54.1 L 29 LYD428 67474.4 0.8 0.08 8 — — — — — — CONT. — 0.7 — — 9.6 — — 42.0 — — LYD484 67135.2 1.0 0.08 7 — — — — — — LYD484 67135.3 1.0 0.21 5 — — — 64.6 0.05 6 LYD470 67126.7 1.1 0.06 17 — — — 72.5 L 20 LYD470 67127.3 — — — — — — 61.9 0.25 2 LYD459 67116.4 1.0 0.22 5 — — — — — — LYD414 67089.4 1.0 L 7 — — — — — — LYD414 67091.1 1.0 0.25 4 — — — — — — LYD387 67317.4 1.1 L 16 11.8 0.17 7 75.4 0.06 24 LYD347 67845.1 1.0 0.27 3 — — — — — — LYD347 67848.2 1.0 0.04 7 — — — — — — LYD341 67054.2 1.0 0.16 3 — — — — — — LYD338 67442.3 1.1 L 15 11.5 0.25 4 73.2 0.12 21 LYD337 66994.3 1.0 0.29 4 — — — 62.8 0.12 4 LYD337 66995.5 — — — — — — 65.5 0.23 8 LYD322 66884.2 1.0 L 13 — — — 68.6 L 13 LYD322 66887.1 — — — — — — 66.0 0.02 9 LYD307 66975.3 — — — — — — 65.0 0.05 7 LYD307 66975.4 1.0 0.02 6 — — — — — — LYD307 66976.3 1.0 L 7 — — — — — — LYD307 66977.3 1.0 0.07 13 — — — 69.9 0.13 15 LYD303 67300.6 1.0 0.14 4 — — — — — — LYD293 66958.1 1.0 0.09 4 — — — — — — CONT. — 0.9 — — 11.0 — — 60.7 — — LYD410 67546.3 — — — 10.8 0.12 11  — — — LYD409 67467.5 0.8 0.01 8 — — — — — — LYD409 67468.1 0.8 0.21 6 — — — — — — LYD405 67694.4 — — — 10.1 0.10 3 — — — LYD405 67697.2 — — — 9.9 0.28 2 — — — LYD379 67678.1 0.8 0.02 8 10.1 0.10 3 51.1 0.13 11 LYD372 67673.3 — — — 10.1 0.12 4 — — — LYD348 67850.1 — — — 10.0 0.16 3 — — — LYD335 67558.2 — — — 10.1 0.28 3 — — — CONT. — 0.8 — — 9.7 — — 45.9 — — LYD489 67785.4 1.0 L 13 — — — 52.0 0.18 6 LYD489 67787.3 — — — 9.5 L 6 — — — LYD483 68056.5 1.0 0.25 6 — — — — — — LYD472 67330.6 1.0 0.02 8 — — — — — — LYD472 67332.4 1.0 0.03 12 — — — 54.0 0.18 10 LYD456 67964.1 — — — 9.4 0.17 5 — — — LYD456 67966.3 1.0 0.07 6 — — — 53.4 0.06 8 LYD456 67967.4 0.9 0.25 4 9.3 0.26 4 51.5 0.14 5 LYD423 68216.3 — — — 9.2 0.19 3 — — — LYD423 68218.3 — — — 9.4 0.17 5 — — — LYD422 68103.3 1.0 0.16 11 — — — — — — LYD422 68103.4 1.0 0.01 9 — — — — — — LYD417 68042.2 — — — 9.4 0.17 5 — — — LYD417 68043.1 0.9 0.10 5 — — — — — — LYD417 68043.5 1.0 0.23 6 — — — — — — LYD392 68032.2 1.0 0.12 15 — — — 53.4 0.21 8 LYD392 68033.3 1.0 0.13 16 9.4 0.09 5 58.1 L 18 LYD392 68035.1 1.0 0.29 8 — — — — — — LYD376 68025.1 — — — 9.2 0.15 3 — — — LYD376 68025.3 — — — 9.1 0.24 2 — — — LYD376 68026.5 — — — 9.2 0.15 3 — — — LYD365 68092.4 1.0 0.02 8 — — — 52.8 0.13 7 LYD365 68092.5 1.1 0.08 16 9.6 0.12 7 57.9 0.22 18 LYD365 68093.2 1.0 0.07 15 9.2 0.06 3 53.3 0.17 8 LYD359 67946.3 1.0 0.01 10 9.2 0.19 3 51.7 0.29 5 LYD359 67947.2 1.0 0.19 8 — — — — — — LYD359 67949.4 — — — 9.7 0.22 8 — — — LYD351 68126.2 1.0 L 14 — — — 55.8 L 13 LYD351 68129.3 1.0 0.04 7 — — — — — — LYD351 68129.5 1.0 0.26 10 — — — 52.4 0.14 6 LYD306 66971.1 1.0 L 13 — — — 56.4 L 14 LYD299 68115.4 — — — 9.4 0.09 5 — — — LYD299 68115.7 1.1 L 21 — — — 57.4 L 17 CONT. — 0.9 — — 9.0 — — 49.2 — — LYD506 67144.2 1.0 0.02 16 11.4 0.26 6 67.1 0.01 19 LYD506 67146.2 1.1 0.19 18 11.8 0.30 8 70.2 0.10 24 LYD504 67136.2 1.0 0.23 7 11.5 0.30 6 63.0 0.04 12 LYD504 67136.3 1.0 0.04 15 12.2 0.02 12  69.6 L 23 LYD504 67138.1 — — — — — — 62.5 0.16 11 LYD504 67139.1 1.0 0.02 17 11.6 L 7 69.0 0.02 22 LYD504 67140.1 — — — 11.4 0.05 5 61.8 0.13 9 LYD466 67119.4 1.0 0.13 8 — — — 61.0 0.24 8 LYD442 67104.3 1.0 0.14 15 11.4 0.22 5 69.3 0.20 23 LYD440 66902.1 1.0 0.12 12 — — — 66.3 0.08 17 LYD440 66902.2 1.0 0.06 12 11.1 0.20 2 65.6 0.08 16 LYD440 66905.1 — — — 11.1 0.20 2 — — — LYD440 66906.1 1.0 0.06 12 11.3 0.02 4 67.4 L 19 LYD432 67959.2 1.0 0.14 15 11.4 0.26 6 69.2 0.22 22 LYD432 67961.2 1.0 0.07 11 — — — 67.5 L 19 LYD425 67454.3 — — — 11.6 L 7 62.8 0.05 11 LYD425 67454.5 1.0 0.24 11 — — — 64.7 0.15 15 LYD408 67304.1 1.1 0.01 19 11.8 L 8 74.3 L 32 LYD408 67305.6 1.1 L 23 — — — 74.5 0.07 32 LYD408 67306.2 1.0 0.13 9 11.4 0.10 6 63.4 0.09 12 LYD401 67084.2 1.0 0.11 9 — — — 60.9 0.17 8 LYD375 67070.2 1.0 0.26 9 — — — 64.0 0.05 13 LYD375 67073.2 1.1 0.02 19 — — — 65.9 0.03 17 LYD342 67059.4 1.0 0.07 11 — — — 64.0 0.03 13 LYD342 67062.1 1.0 0.01 18 12.0 0.16 11  72.6 L 28 LYD329 67275.1 — — — — — — 59.6 0.26 6 LYD329 67277.4 — — — — — — 65.4 0.04 16 LYD320 67040.2 — — — 11.6 L 7 59.7 0.24 6 LYD320 67043.1 1.0 0.20 7 — — — 60.1 0.20 6 LYD318 66980.3 — — — — — — 60.8 0.14 8 LYD318 66980.5 — — — — — — 62.6 0.08 11 LYD318 66982.1 — — — 11.6 L 7 63.8 0.03 13 LYD318 66983.4 1.0 0.03 15 12.3 0.08 14  70.6 L 25 LYD316 67436.1 1.0 0.24 11 11.7 0.05 8 64.7 0.02 14 LYD316 67437.2 1.0 0.05 12 — — — 65.1 0.02 15 LYD316 67439.1 1.0 0.01 17 11.8 0.10 8 69.6 L 23 LYD298 66963.4 — — — 11.8 0.21 8 — — — LYD292 66998.3 1.0 0.01 17 11.6 0.01 7 68.3 L 21 LYD292 66999.2 1.1 0.04 24 11.6 0.13 7 74.8 0.05 32 LYD292 66999.4 1.0 0.16 12 — — — 64.7 0.14 15 LYD292 67000.1 1.1 0.02 21 — — — 75.6 0.01 34 CONT. — 0.9 — — 10.8 — — 56.5 — — LYD362 67543.5 0.75 0.12 10.2 — — — — — — LYD362 67541.3 0.75 0.13 10 — — — — — — LYD362 67538.2 0.74 0.15 9.3 — — — — — — LYD362 67543.3 0.72 0.32 6.3 — — — — — — LYD362 67543.6 0.72 0.34 6.1 — — — — — — LYD366 67810.1 0.74 0.18 8.5 — — — — — — LYD366 67812.5 0.73 0.29 6.8 — — — — — — LYD386 67860.3 0.71 0.47 4.5 — — — — — — LYD386 67856.1 0.71 0.50 4.2 — — — — — — CONT. — 0.68 — — — — — — — — LYD362 67543.5 0.74 0.06 12.3 — — — — — — LYD362 67541.3 0.74 0.06 12.2 — — — — — — LYD362 67538.2 0.74 0.07 12.0 — — — — — — LYD362 67543.3 0.73 0.11 10.6 — — — — — — LYD362 67543.6 0.73 0.11 10.5 — — — — — — LYD366 67810.1 0.72 0.16 9.2 — — — — — — LYD366 67812.5 0.72 0.19 8.4 — — — — — — LYD366 67808.2 0.71 0.27 7.0 — — — — — — LYD366 67812.1 0.70 0.33 6.1 — — — — — — LYD366 67810.4 0.70 0.38 5.6 — — — — — — LYD386 67860.3 0.70 0.39 5.3 — — — — — — LYD386 67856.1 0.69 0.41 5.2 — — — — — — CONT. — 0.66 — — — — — — — — LYD434 67978.2 — — — 9.7 0.22   3.1 — — — LYD434 67977.3 — — — 9.6 0.32   2.1 — — — CONT. — — — — 9.4 — — — — — Table 57. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “P-val.”—p-value, L—p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 14467). “—” = results are still unavailable.

TABLE 58 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter RGR Of Leaf RGR Of Plot RGR Of Rosette Gene Number Coverage Diameter Name Event # Ave. P-Val. % Incr. Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD446 68109.4 — — — 8.2 0.23 15 0.5 0.16 9 LYD446 68110.1 — — — 8.4 0.13 18 — — — LYD443 68163.1 — — — 8.3 0.15 16 0.5 0.14 8 LYD443 68164.2 — — — 8.7 0.07 21 0.5 0.13 8 LYD443 68165.3 — — — 8.4 0.11 18 0.5 0.05 11  LYD436 68073.1 — — — — — — 0.5 0.26 7 LYD436 68073.3 — — — 8.7 0.07 22 0.5 0.20 7 LYD436 68075.3 — — — 8.9 0.07 24 0.5 0.09 12  LYD416 67904.3 0.7 0.29 16 — — — — — — LYD416 67907.6 — — — — — — 0.5 0.22 7 LYD391 68160.4 — — — 9.2 0.02 29 0.5 0.01 15  LYD388 68096.2 — — — 8.5 0.09 19 0.5 0.09 9 LYD388 68098.2 — — — 9.3 0.01 30 0.5 0.02 12  LYD388 68098.3 — — — — — — 0.5 0.18 7 LYD388 68098.4 — — — 8.7 0.08 22 0.5 0.14 9 LYD367 68066.1 — — — 8.1 0.28 14 0.5 0.19 9 LYD367 68066.5 — — — 9.2 0.02 29 0.5 0.02 13  LYD367 68066.6 — — — 8.5 0.15 19 0.5 0.20 8 LYD367 68068.5 — — — 8.4 0.16 17 0.5 0.15 8 LYD364 68018.3 — — — 8.2 0.23 15 0.5 0.10 10  LYD364 68018.4 — — — 8.1 0.22 14 0.5 0.12 9 LYD364 68020.5 — — — 9.8 L 37 0.5 0.03 12  LYD364 68022.1 — — — 8.3 0.15 16 — — — LYD360 68061.1 — — — 8.7 0.06 22 0.5 0.02 12  LYD360 68061.2 — — — — — — 0.5 0.26 6 LYD360 68063.2 — — — — — — 0.5 0.24 6 LYD357 68228.1 — — — — — — 0.5 0.13 8 LYD354 68133.4 — — — 8.2 0.22 14 — — — LYD354 68133.6 — — — 8.0 0.29 12 — — — LYD354 68134.8 — — — 8.2 0.21 15 — — — LYD349 68085.5 — — — 10.3  L 45 0.5 0.02 12  LYD308 66881.2 — — — 8.4 0.12 18 — — — LYD295 67972.2 — — — 8.5 0.11 19 0.5 0.03 12  LYD295 67972.4 — — — 8.2 0.18 15 — — — CONT. — 0.6 — — 7.1 — — 0.5 — — LYD513 67217.3 — — — 6.0 0.05 22 0.4 0.06 10  LYD512 67209.1 — — — 5.6 0.26 13 0.3 0.28 7 LYD512 67209.4 — — — — — — 0.3 0.27 6 LYD482 67334.1 — — — — — — 0.3 0.28 6 LYD475 67204.4 — — — 5.9 0.08 19 0.4 0.04 11  LYD472 67332.1 — — — 6.1 0.04 23 0.4 0.05 11  LYD472 67332.3 — — — — — — 0.3 0.26 7 LYD472 67332.4 — — — 6.1 0.04 23 0.3 0.14 8 LYD466 67121.1 — — — 5.9 0.07 20 0.4 0.06 10  LYD451 67187.7 — — — — — — 0.3 0.19 7 LYD451 67188.1 — — — 5.8 0.13 18 0.4 0.02 14  LYD451 67188.4 — — — 5.8 0.12 17 0.3 0.26 6 LYD445 67353.2 — — — 5.6 0.19 14 0.3 0.26 6 LYD439 67094.1 — — — 5.5 0.26 12 0.3 0.23 8 LYD439 67094.3 — — — 5.8 0.12 18 0.3 0.13 8 LYD439 67095.6 — — — 5.6 0.22 13 — — — LYD415 67266.6 — — — — — — 0.3 0.27 7 LYD382 67174.1 — — — 5.6 0.20 14 — — — LYD382 67175.2 — — — 5.7 0.15 16 — — — LYD382 67176.3 — — — — — — 0.3 0.14 9 LYD324 67167.1 — — — — — — 0.3 0.23 7 LYD321 67280.1 — — — — — — 0.3 0.24 7 LYD321 67283.1 — — — 5.8 0.10 18 0.4 0.09 9 LYD321 67283.3 — — — — — — 0.4 0.08 10  LYD321 67283.4 — — — 6.8 L 37 0.4 L 16  LYD302 67414.3 — — — 5.6 0.22 13 0.3 0.17 7 LYD302 67416.3 — — — 5.6 0.20 14 0.4 0.09 9 LYD296 67358.6 — — — 6.1 0.05 23 0.4 0.07 12  LYD296 67359.3 — — — — — — 0.3 0.25 6 LYD296 67360.1 — — — — — — 0.3 0.27 6 CONT. — — — — 4.9 — — 0.3 — — LYD517 67222.1 — — — 4.1 0.30 15 0.3 0.19 11  LYD515 67151.1 — — — 4.2 0.20 18 0.4 0.11 12  LYD515 67151.4 — — — — — — 0.3 0.30 8 LYD515 67152.4 — — — 4.7 0.04 31 0.4 0.05 15  LYD502 67341.5 — — — 4.1 0.30 15 0.3 0.21 9 LYD498 67252.3 — — — 4.2 0.20 18 0.3 0.20 9 LYD498 67254.3 — — — 4.2 0.20 18 0.4 0.07 14  LYD492 67364.5 — — — — — — 0.3 0.28 8 LYD454 67192.5 — — — 4.2 0.19 19 — — — LYD450 67178.3 — — — 4.1 0.29 15 — — — LYD450 67182.2 — — — 4.2 0.18 19 0.3 0.25 9 LYD397 67324.2 — — — 4.6 0.05 29 0.4 0.08 14  LYD323 67286.1 — — — 4.2 0.23 17 0.3 0.20 9 LYD323 67287.3 — — — 4.2 0.22 18 0.3 0.24 9 LYD323 67288.2 — — — 4.2 0.28 18 — — — LYD312 67256.4 — — — 4.6 0.05 30 0.3 0.21 9 LYD312 67256.5 — — — 4.2 0.24 17 — — — LYD301 67347.2 — — — 4.5 0.06 28 0.4 0.01 20  LYD298 66964.4 — — — 4.4 0.08 25 0.4 0.07 13  LYD298 66966.2 — — — 4.1 0.29 15 — — — CONT. — — — — 3.6 — — 0.3 — — LYD508 67824.3 — — — 5.8 0.11 19 — — — LYD479 67727.4 — — — 6.3 0.03 28 0.3 0.10 16  LYD428 67473.3 0.8 0.20 17 6.4 0.02 31 0.3 0.07 17  LYD346 67606.2 — — — 5.6 0.29 14 — — — CONT. — 0.6 — — 4.9 — — 0.3 — — LYD470 67126.7 — — — 8.7 0.15 19 0.4 0.02 12  LYD459 67116.4 — — — — — — 0.4 0.24 6 LYD387 67316.1 — — — — — — 0.4 0.12 9 LYD387 67317.4 0.8 0.25 12 9.3 0.04 26 0.4 L 15  LYD347 67848.2 — — — — — — 0.4 0.15 7 LYD338 67442.3 — — — 9.0 0.09 22 0.4 0.02 12  LYD337 66995.4 — — — — — — 0.4 0.07 10  LYD337 66995.5 — — — — — — 0.4 0.10 8 LYD322 66884.1 — — — — — — 0.4 0.24 6 LYD322 66884.2 — — — 8.4 0.26 14 0.4 0.17 7 LYD322 66886.6 — — — — — — 0.4 0.12 8 LYD322 66887.1 — — — — — — 0.4 0.12 8 LYD307 66975.3 — — — — — — 0.4 0.11 8 LYD307 66975.4 — — — — — — 0.4 0.25 6 LYD307 66976.3 — — — — — — 0.4 0.12 8 LYD307 66977.3 — — — 8.6 0.17 17 0.4 0.06 10  LYD303 67298.1 — — — — — — 0.4 0.20 7 LYD303 67300.6 — — — — — — 0.4 0.19 7 CONT. — 0.7 — — 7.4 — — 0.4 — — LYD410 67546.3 0.8 0.22 14 — — — — — — LYD379 67678.1 — — — 6.1 0.29 12 0.3 0.25 9 CONT. — 0.7 — — 5.5 — — 0.3 — — LYD489 67787.3 0.7 0.14 24 — — — — — — LYD483 68054.4 0.6 0.29 16 — — — — — — LYD471 68050.2 0.7 0.20 22 — — — — — — LYD456 67964.1 0.7 0.22 21 — — — — — — LYD456 67967.4 0.6 0.24 19 — — — 0.5 0.17 11  LYD423 68218.3 0.7 0.09 26 — — — — — — LYD422 68103.4 — — — 7.3 0.28 13 — — — LYD392 68033.3 — — — 7.7 0.13 19 — — — LYD365 68092.5 0.6 0.24 19 7.7 0.13 19 0.5 0.14 12  LYD359 67949.4 0.7 0.19 22 — — — — — — LYD351 68126.2 — — — 7.4 0.24 14 — — — LYD306 66971.1 — — — 7.4 0.21 15 — — — LYD299 68115.7 — — — 7.6 0.15 18 0.5 0.28 8 CONT. — 0.5 — — 6.5 — — 0.4 — — LYD506 67144.2 0.8 0.25 10 8.3 0.10 22 0.4 0.25 9 LYD506 67146.2 — — — 8.5 0.07 24 — — — LYD504 67136.2 — — — 7.8 0.26 14 — — — LYD504 67136.3 0.8 0.09 16 8.6 0.06 25 0.4 0.17 11  LYD504 67139.1 — — — 8.4 0.08 23 0.4 0.18 11  LYD442 67104.3 — — — 8.6 0.06 26 — — — LYD440 66902.1 — — — 8.1 0.16 19 — — — LYD440 66902.2 — — — 8.0 0.23 16 0.4 0.26 9 LYD440 66906.1 — — — 8.2 0.15 20 — — — LYD432 67959.2 — — — 8.5 0.08 24 0.4 0.27 9 LYD432 67961.2 — — — 8.3 0.12 21 — — — LYD425 67454.3 0.8 0.22 11 7.8 0.25 14 — — — LYD425 67454.5 — — — 8.0 0.21 16 — — — LYD408 67304.1 0.8 0.21 12 9.1 0.02 33 0.4 0.21 10  LYD408 67305.6 — — — 9.0 0.02 32 — — — LYD401 67086.2 — — — 7.8 0.27 14 — — — LYD375 67070.2 — — — 8.0 0.19 17 — — — LYD375 67073.2 — — — 8.1 0.16 19 — — — LYD342 67059.4 — — — 7.9 0.22 16 — — — LYD342 67062.1 — — — 8.9 0.03 30 — — — LYD329 67277.4 — — — 8.0 0.18 17 — — — LYD320 67040.2 0.8 0.28 11 — — — — — — LYD318 66980.7 — — — 7.8 0.29 14 — — — LYD318 66982.1 — — — 7.9 0.25 15 — — — LYD318 66983.4 — — — 8.6 0.06 25 — — — LYD316 67436.1 0.8 0.11 15 8.1 0.17 18 — — — LYD316 67437.2 — — — 8.1 0.18 18 0.4 0.29 8 LYD316 67439.1 0.8 0.15 14 8.5 0.07 24 — — — LYD298 66963.4 0.9 0.07 18 7.9 0.28 15 — — — LYD292 66998.3 — — — 8.4 0.09 22 — — — LYD292 66999.2 — — — 9.2 0.01 34 0.4 0.26 9 LYD292 66999.4 — — — 8.0 0.21 17 — — — LYD292 67000.1 — — — 9.3 0.01 36 0.4 0.27 9 CONT. — 0.7 — — 6.9 — — 0.4 — — Table 58. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “P-val.”—p-value, L—p < 0.01. RGR = relative growth rate. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 14467). “—” = results are still unavailable.

TABLE 59 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter Rosette Area Rosette Diameter Harvest Index [cm²] [cm] Gene P- % P- % P- % Name Event # Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD446 68109.4 — — — — — — 5.0 0.26 8 LYD446 68110.1 — — — 7.9 0.03 18 4.9 0.03 6 LYD443 68163.1 — — — 7.8 0.14 17 5.0 0.13 8 LYD443 68164.2 — — — 8.0 0.12 20 5.0 L 7 LYD443 68165.3 — — — 7.9 L 18 5.1 L 9 LYD436 68073.3 — — — 8.0 0.02 21 5.0 L 6 LYD416 67904.3 — — — 7.1 0.03  6 4.7 0.29 1 LYD416 67907.6 — — — — — — 4.7 0.24 1 LYD391 68156.4 — — — 7.2 L  9 4.8 0.12 3 LYD391 68160.4 — — — 8.6 0.09 28 5.3 0.14 13  LYD388 68096.2 — — — 7.9 L 19 5.0 L 8 LYD388 68098.2 — — — 8.6 L 29 5.2 L 12  LYD388 68098.3 — — — 7.2 0.14  9 4.9 0.22 5 LYD388 68098.4 — — — — — — 5.1 0.17 9 LYD367 68066.5 — — — 8.6 0.14 29 5.2 0.07 11  LYD364 68018.4 — — — 7.5 0.03 13 4.9 0.06 5 LYD364 68020.1 — — — 6.9 0.29  3 — — — LYD364 68020.5 — — — 9.1 L 36 5.2 L 12  LYD364 68022.1 — — — 7.8 0.15 17 4.9 0.16 6 LYD361 68147.1 — — — 7.0 0.25  5 — — — LYD360 68061.1 — — — 8.1 0.02 22 5.2 0.03 11  LYD360 68063.2 — — — 7.3 0.26  9 4.8 0.12 3 LYD357 68228.1 — — — 7.2 0.20  8 4.8 L 4 LYD354 68133.4 — — — 7.7 0.11 16 4.9 0.29 5 LYD349 68085.3 — — — — — — 4.7 0.14 2 LYD349 68085.5 — — — 9.6 0.08 44 5.3 0.04 14  LYD308 66881.2 — — — 7.9 0.02 18 4.9 0.02 5 LYD295 67972.2 — — — 7.9 0.17 18 5.0 0.02 8 LYD295 67972.4 — — — 7.7 0.20 16 4.9 0.22 6 CONT. — — — — 6.7 — — 4.7 — — LYD513 67217.3 — — — 6.2 L 22 4.3 0.04 10  LYD512 67209.1 — — — — — — 4.2 0.24 8 LYD482 67334.1 — — — — — — 4.2 0.24 7 LYD482 67335.3 — — — — — — 4.0 0.24 3 LYD482 67336.1 — — — — — — 4.1 0.23 4 LYD475 67202.3 — — — — — — 4.1 0.21 6 LYD475 67204.4 — — — 6.0 L 18 4.2 0.03 9 LYD472 67332.1 — — — 6.2 0.06 23 4.3 0.03 10  LYD472 67332.3 — — — — — — 4.2 0.21 7 LYD472 67332.4 — — — 6.2 L 23 4.4 L 11  LYD466 67121.1 — — — 6.1 L 21 4.3 L 11  LYD452 67106.2 — — — 5.4 0.20  7 — — — LYD451 67187.9 — — — 5.5 0.09  8 — — — LYD451 67188.1 — — — — — — 4.3 0.20 9 LYD451 67188.4 — — — 5.9 0.07 17 4.1 0.12 6 LYD445 67353.1 — — — 5.4 0.27  7 — — — LYD445 67353.2 — — — 5.9 L 16 4.2 0.01 8 LYD445 67354.5 — — — 5.3 0.29  6 — — — LYD439 67094.1 — — — — — — 4.2 0.22 7 LYD439 67094.3 — — — 5.9 0.06 17 4.2 0.03 8 LYD439 67095.2 — — — — — — 4.1 0.16 6 LYD439 67095.6 — — — 5.7 0.02 13 4.2 0.02 6 LYD415 67262.1 — — — 5.6 0.21 11 4.2 L 8 LYD415 67264.5 — — — 5.4 0.13  7 4.0 0.21 3 LYD382 67174.1 — — — 5.7 0.19 13 — — — LYD382 67175.2 — — — 5.9 0.16 17 4.2 0.05 7 LYD382 67176.3 — — — — — — 4.2 0.06 7 LYD339 67247.3 — — — — — — 4.0 0.25 2 LYD324 67167.1 — — — — — — 4.1 0.30 4 LYD321 67283.1 — — — 6.0 0.01 18 4.2 0.07 8 LYD321 67283.3 — — — — — — 4.2 0.13 6 LYD321 67283.4 — — — 6.9 0.04 36 4.6 0.03 19  LYD302 67414.3 — — — 5.8 0.03 14 4.2 L 8 LYD302 67416.3 — — — 5.7 0.02 12 4.2 0.02 7 LYD296 67358.6 — — — 6.3 0.14 24 4.4 0.24 12  LYD296 67359.3 — — — — — — 4.2 0.01 7 LYD296 67360.1 — — — — — — 4.1 0.08 5 CONT. — — — — 5.1 — — 3.9 — — LYD517 67221.3 — — — 3.8 0.14  6 3.6 0.03 7 LYD517 67221.5 — — — — — — 3.4 0.29 3 LYD515 67151.1 — — — 4.2 0.08 17 3.8 0.02 12  LYD515 67151.4 — — — — — — 3.7 0.28 9 LYD515 67151.6 — — — — — — 3.6 0.05 7 LYD515 67152.4 — — — 4.6 L 29 3.8 0.03 14  LYD502 67340.4 — — — 4.0 0.09 13 3.6 0.12 6 LYD502 67341.5 — — — 4.1 0.04 15 3.7 0.02 10  LYD502 67342.6 — — — 3.9 0.02 11 3.5 0.09 5 LYD498 67252.3 — — — 4.2 L 17 3.7 0.01 9 LYD498 67254.1 — — — 3.9 0.06 10 3.5 0.06 6 LYD498 67254.3 — — — 4.1 0.01 16 3.7 L 10  LYD492 67364.5 — — — 3.9 0.20 11 3.6 0.20 7 LYD474 67199.1 — — — 3.9 0.05  9 — — — LYD454 67192.5 — — — 4.2 0.02 18 3.6 0.02 9 LYD450 67178.3 — — — 4.1 0.02 14 3.6 0.07 7 LYD450 67180.2 — — — 4.0 0.27 11 3.6 0.18 7 LYD450 67182.2 — — — 4.2 0.01 18 3.7 0.06 10  LYD428 67472.2 — — — — — — 3.5 0.11 5 LYD397 67322.1 — — — 3.8 0.28  6 — — — LYD397 67324.2 — — — 4.5 0.04 28 3.8 L 14  LYD323 67286.1 — — — 4.1 0.29 16 3.7 0.08 9 LYD323 67287.3 — — — 4.1 L 16 3.6 0.02 7 LYD312 67256.4 — — — 4.6 0.08 30 3.8 0.09 13  LYD312 67256.5 — — — 4.1 L 16 3.6 0.02 7 LYD310 67161.1 — — — 4.0 0.04 12 3.5 0.29 3 LYD310 67164.1 — — — 3.8 0.08  7 3.5 0.22 3 LYD301 67347.2 — — — 4.4 0.01 25 3.8 0.05 14  LYD301 67347.4 — — — 4.0 0.13 12 3.6 0.08 6 LYD298 66964.4 — — — 4.4 0.15 24 3.8 0.01 14  LYD298 66966.2 — — — 4.1 L 15 3.6 0.02 7 CONT. — — — — 3.5 — — 3.4 — — LYD508 67823.1 0.4 0.23 14 — — — — — — LYD508 67823.2 0.4 0.29 7 5.6 0.13  7 4.0 0.23 2 LYD508 67823.4 0.4 0.14 11 — — — — — — LYD508 67824.3 — — — 6.2 0.08 18 4.2 0.11 6 LYD503 67526.2 0.4 0.08 17 — — — — — — LYD503 67529.1 0.4 0.24 7 — — — — — — LYD503 67529.3 0.4 0.27 8 — — — — — — LYD497 67880.3 0.4 0.30 8 — — — — — — LYD497 67883.4 — — — 5.8 0.03 10 4.1 0.08 5 LYD491 67876.2 0.4 0.29 20 — — — — — — LYD489 67787.4 0.4 0.16 9 — — — — — — LYD479 67727.4 — — — 6.7 0.21 28 4.4 L 12  LYD458 67922.2 0.4 0.29 11 — — — — — — LYD435 67707.3 0.4 0.14 9 — — — — — — LYD435 67708.2 0.4 0.03 15 — — — — — — LYD433 67700.1 0.4 0.04 21 — — — — — — LYD433 67704.4 0.4 0.19 9 — — — — — — LYD428 67473.3 0.4 0.07 12 6.8 L 29 4.4 L 12  LYD428 67474.3 0.4 0.08 14 — — — — — — LYD305 67535.5 0.4 0.29 7 — — — — — — CONT. — 0.4 — — 5.2 — — 3.9 — — LYD484 67135.3 — — — 8.1 0.05  6 4.9 0.20 3 LYD470 67126.7 — — — 9.1 L 20 5.2 0.04 9 LYD470 67127.3 — — — 7.7 0.25  2 4.8 0.20 2 LYD459 67116.4 — — — — — — 4.9 0.02 3 LYD387 67317.4 — — — 9.4 0.06 24 5.4 L 14  LYD338 67442.3 — — — 9.2 0.12 21 5.3 L 11  LYD337 66994.3 — — — 7.8 0.12  4 — — — LYD337 66995.4 — — — — — — 5.0 0.27 5 LYD337 66995.5 — — — 8.2 0.23  8 — — — LYD322 66884.1 — — — — — — 4.9 0.03 3 LYD322 66884.2 — — — 8.6 L 13 5.0 L 5 LYD322 66886.6 — — — — — — 4.9 0.04 4 LYD322 66887.1 — — — 8.3 0.02  9 5.0 0.13 5 LYD307 66975.3 — — — 8.1 0.05  7 4.9 0.02 4 LYD307 66975.4 — — — — — — 4.9 0.11 2 LYD307 66977.3 — — — 8.7 0.13 15 5.1 0.21 8 CONT. — — — — 7.6 — — 4.7 — — LYD453 67484.1 0.4 0.07 12 — — — — — — LYD453 67485.2 0.4 0.07 11 — — — — — — LYD453 67485.5 0.4 0.10 15 — — — — — — LYD410 67546.1 0.4 0.25 6 — — — — — — LYD410 67548.3 0.4 0.08 11 — — — — — — LYD409 67468.2 0.4 0.29 8 — — — — — — LYD409 67469.1 0.4 0.29 5 — — — — — — LYD405 67694.4 0.4 0.12 9 — — — — — — LYD405 67695.2 0.5 L 22 — — — — — — LYD405 67696.2 0.4 0.02 16 — — — — — — LYD405 67697.2 0.4 0.16 7 — — — — — — LYD404 67690.2 0.4 0.18 8 — — — — — — LYD404 67690.4 0.4 0.24 16 — — — — — — LYD403 67770.3 0.4 0.20 7 — — — — — — LYD402 67762.1 0.4 0.19 8 — — — — — — LYD402 67765.3 0.4 0.21 7 — — — — — — LYD396 67754.1 0.4 0.11 17 — — — — — — LYD396 67759.3 0.4 0.04 17 — — — — — — LYD379 67678.1 — — — 6.4 0.13 11 4.2 0.02 5 LYD372 67673.4 — — — — — — 4.1 0.12 3 LYD366 67810.4 0.4 0.19 16 — — — — — — LYD366 67812.1 0.4 0.12 8 — — — — — — LYD362 67538.2 0.4 0.03 13 — — — — — — LYD362 67543.5 0.4 0.29 6 — — — — — — LYD362 67543.6 0.4 0.01 19 — — — — — — LYD355 67641.3 0.4 0.02 15 — — — — — — LYD355 67641.4 0.4 0.11 9 — — — — — — LYD355 67643.3 0.4 0.05 12 — — — — — — LYD348 67851.6 0.4 0.25 6 — — — — — — LYD348 67851.7 0.4 L 18 — — — — — — LYD348 67853.1 0.5 0.08 24 — — — — — — LYD348 67854.3 0.4 0.02 16 — — — — — — LYD347 67844.2 0.4 0.10 9 — — — — — — LYD347 67848.2 0.4 0.10 9 — — — — — — CONT. — 0.4 — — 5.7 — — 4.0 — — LYD489 67785.4 — — — 6.5 0.18  6 — — — LYD472 67332.4 — — — 6.7 0.18 10 — — — LYD458 67922.1 — — — — — — 4.6 0.27 3 LYD456 67966.3 — — — 6.7 0.06  8 4.7 0.14 4 LYD456 67967.4 — — — 6.4 0.14  5 4.7 0.18 4 LYD422 68103.3 — — — — — — 4.7 0.15 4 LYD417 68045.3 — — — — — — 4.6 0.28 3 LYD392 68032.2 — — — 6.7 0.21  8 4.7 0.09 6 LYD392 68033.3 — — — 7.3 L 18 4.8 0.14 6 LYD365 68092.4 — — — 6.6 0.13  7 4.6 0.26 3 LYD365 68092.5 — — — 7.2 0.22 18 4.9 0.01 9 LYD365 68093.2 — — — 6.7 0.17  8 4.7 0.27 4 LYD359 67946.3 — — — 6.5 0.29  5 — — — LYD351 68126.2 — — — 7.0 L 13 4.7 0.09 5 LYD351 68129.5 — — — 6.5 0.14  6 — — — LYD306 66971.1 — — — 7.0 L 14 4.8 0.06 6 LYD299 68115.7 — — — 7.2 L 17 4.8 0.04 7 CONT. — — — — 6.2 — — 4.5 — — LYD506 67144.2 — — — 8.4 0.01 19 5.1 L 9 LYD506 67146.2 — — — 8.8 0.10 24 5.1 0.28 9 LYD504 67136.2 — — — 7.9 0.04 12 4.9 0.06 5 LYD504 67136.3 — — — 8.7 L 23 5.1 L 10  LYD504 67138.1 — — — 7.8 0.16 11 — — — LYD504 67139.1 — — — 8.6 0.02 22 5.1 0.02 10  LYD504 67140.1 — — — 7.7 0.13  9 4.8 0.27 3 LYD466 67119.4 — — — 7.6 0.24  8 — — — LYD442 67104.3 — — — 8.7 0.20 23 5.1 0.17 9 LYD440 66902.1 — — — 8.3 0.08 17 5.0 0.03 6 LYD440 66902.2 — — — 8.2 0.08 16 5.0 0.04 6 LYD440 66906.1 — — — 8.4 L 19 5.0 0.03 7 LYD432 67959.2 — — — 8.6 0.22 22 5.1 0.22 9 LYD432 67961.2 — — — 8.4 L 19 5.1 0.10 9 LYD425 67454.3 — — — 7.9 0.05 11 4.9 0.07 5 LYD425 67454.5 — — — 8.1 0.15 15 4.9 0.22 5 LYD408 67304.1 — — — 9.3 L 32 5.2 0.01 12  LYD408 67305.6 — — — 9.3 0.07 32 5.3 L 14  LYD408 67306.2 — — — 7.9 0.09 12 — — — LYD401 67084.2 — — — 7.6 0.17  8 4.8 0.27 3 LYD401 67086.2 — — — — — — 4.9 0.19 6 LYD375 67070.2 — — — 8.0 0.05 13 4.9 0.05 5 LYD375 67073.2 — — — 8.2 0.03 17 5.0 0.03 7 LYD342 67059.4 — — — 8.0 0.03 13 4.9 0.05 5 LYD342 67062.1 — — — 9.1 L 28 5.1 L 9 LYD329 67275.1 — — — 7.5 0.26  6 — — — LYD329 67277.4 — — — 8.2 0.04 16 5.0 0.25 7 LYD320 67040.2 — — — 7.5 0.24  6 — — — LYD320 67043.1 — — — 7.5 0.20  6 4.8 0.14 4 LYD318 66980.3 — — — 7.6 0.14  8 4.9 0.12 5 LYD318 66980.5 — — — 7.8 0.08 11 4.8 0.17 4 LYD318 66982.1 — — — 8.0 0.03 13 4.9 0.17 4 LYD318 66983.4 — — — 8.8 L 25 5.1 L 10  LYD316 67436.1 — — — 8.1 0.02 14 4.9 0.19 5 LYD316 67437.2 — — — 8.1 0.02 15 5.0 0.10 8 LYD316 67439.1 — — — 8.7 L 23 5.1 0.02 10  LYD311 67425.1 — — — — — — 4.8 0.27 4 LYD292 66998.3 — — — 8.5 L 21 5.0 0.02 7 LYD292 66999.2 — — — 9.3 0.05 32 5.3 L 13  LYD292 66999.4 — — — 8.1 0.14 15 — — — LYD292 67000.1 — — — 9.5 0.01 34 5.2 0.04 11  CONT. — — — — 7.1 — — 4.7 — — Table 59. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L - p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 14467). “—” = results are still unavailable.

TABLE 60 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter Gene Seed Yield [mg] 1000 Seed Weight [mg] Name Event # Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD508 67823.2 459.9 0.08 18 — — — LYD508 67823.4 432.1 0.24 11 — — — LYD508 67824.3 455.4 0.08 17 — — — LYD503 67529.1 430.3 0.25 10 — — — LYD503 67529.3 417.3 0.13 7 — — — LYD497 67883.1 427.1 0.08 9 — — — LYD489 67784.4 413.4 0.18 6 — — — LYD435 67706.1 426.1 0.11 9 — — — LYD435 67708.1 417.9 0.24 7 — — — LYD433 67700.1 487.3 0.01 25 — — — LYD433 67704.4 435.2 0.11 11 — — — LYD428 67473.3 494.4 0.06 27 — — — LYD428 67474.3 444.4 0.20 14 — — — LYD346 67605.4 444.8 0.06 14 — — — CONT. — 390.4 — — — — — LYD453 67485.2 454.1 0.13 7 — — — LYD410 67546.3 454.3 0.06 7 — — — LYD409 67468.2 490.5 0.18 15 — — — LYD405 67695.2 511.4 0.02 20 — — — LYD405 67696.2 534.5 0.28 26 — — — LYD396 67759.5 483.5 L 14 — — — LYD379 67677.1 476.9 0.19 12 — — — LYD366 67812.5 478.3 0.14 12 — — — LYD362 67538.2 499.0 L 17 — — — LYD355 67641.3 470.8 0.08 11 — — — LYD348 67851.7 476.1 0.01 12 — — — LYD348 67853.1 519.8 0.18 22 — — — LYD348 67854.3 472.8 0.29 11 — — — LYD347 67844.2 497.9 L 17 — — — CONT. — 425.5 — — — — — Table 60. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L - p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 14467). “—” = results are still unavailable.

Example 17 Evaluation of Transgenic Arabidopsis for Seed Yield and Plant Growth Rate Under Normal Conditions in Greenhouse Assays Until Bolting (GH-SB Assays)

Assay 2: Plant performance improvement measured until bolting stage: plant biomass and plant growth rate under normal greenhouse conditions (GH-SB Assays)—This assay follows the plant biomass formation and the rosette area growth of plants grown in the greenhouse under normal growth conditions. Transgenic Arabidopsis seeds were sown in agar media supplemented with ½ MS medium and a selection agent (Kanamycin). The T₂ transgenic seedlings were then transplanted to 1.7 trays filled with peat and perlite in a 1:1 ratio. The trays were irrigated with a solution containing of 6 mM inorganic nitrogen in the form of KNO₃ with 1 mM KH₂PO₄, 1 mM MgSO₄, 2 mM CaCl₂ and microelements. All plants were grown in the greenhouse until bolting stage. Plant biomass (the above ground tissue) was weight in directly after harvesting the rosette (plant fresh weight [FW]). Following plants were dried in an oven at 50° C. for 48 hours and weighted (plant dry weight [DW]).

Each construct was validated at its T₂ generation. Transgenic plants transformed with a construct conformed by an empty vector carrying the 35S promoter and the selectable marker was used as control.

The plants were analyzed for their overall size, growth rate, fresh weight and dry matter. Transgenic plants performance was compared to control plants grown in parallel under the same conditions. Mock-transgenic plants expressing the uidA reporter gene (GUS-Intron) or with no gene at all, under the same promoter were used as control.

The experiment was planned in nested randomized plot distribution. For each gene of the invention three to five independent transformation events were analyzed from each construct.

Digital imaging—A laboratory image acquisition system, which consists of a digital reflex camera (Canon EOS 300D) attached with a 55 mm focal length lens (Canon EF-S series), mounted on a reproduction device (Kaiser RS), which includes 4 light units (4×150 Watts light bulb) was used for capturing images of plant samples.

The image capturing process was repeated every 2 days starting from day 1 after transplanting till day 15. Same camera, placed in a custom made iron mount, was used for capturing images of larger plants sawn in white tubs in an environmental controlled greenhouse. The tubs were square shape include 1.7 liter trays. During the capture process, the tubes were placed beneath the iron mount, while avoiding direct sun light and casting of shadows.

An image analysis system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.39 [Java based image processing program which was developed at the U.S. National Institutes of Health and freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Images were captured in resolution of 10 Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute).

Leaf analysis—Using the digital analysis leaves data was calculated, including leaf number, rosette area, rosette diameter, and leaf blade area.

Vegetative growth rate: the relative growth rate (RGR) of leaf number (Formula IX, described above), rosette area (Formula VIII described above) and plot coverage (Formula XIII, described above) were calculated using the indicated formulas.

Plant Fresh and Dry weight—On about day 80 from sowing, the plants were harvested and directly weight for the determination of the plant fresh weight (FW) and left to dry at 50° C. in a drying chamber for about 48 hours before weighting to determine plant dry weight (DW).

Statistical analyses—To identify outperforming genes and constructs, results from the independent transformation events tested were analyzed separately. Data was analyzed using Student's t-test and results are considered significant if the p value was less than 0.1. The JMP statistics software package was used (Version 5.2.1, SAS Institute Inc., Cary, N.C., USA).

Experimental Results

Tables 61-64 summarize the observed phenotypes of transgenic plants expressing the genes constructs using the GH-SB Assays.

The genes listed in Tables 61-64 improved plant performance when grown at normal conditions. These genes produced larger plants with a larger photosynthetic area, biomass (fresh weight, dry weight, rosette diameter, rosette area and plot coverage), relative growth rate, blade relative area and petiole relative area. The genes were cloned under the regulation of a constitutive At6669 promoter (SEQ ID NO:14467). The evaluation of each gene was performed by testing the performance of different number of events. Event with p-value<0.1 was considered statistically significant.

TABLE 61 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter Dry Weight [mg] Fresh Weight [mg] Leaf Number Gene P- % P- % P- % Name Event # Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD511 67774.3 426.2 0.21  7 — — — — — — LYD441 67714.3 — — — — — — 10.2  0.11 3 LYD410 67546.2 431.2 0.23  8 5181.2 0.14 7 — — — LYD410 67546.3 — — — — — — 10.6  0.13 7 LYD396 67754.1 426.2 0.22  7 5081.2 0.25 5 10.6  0.14 7 LYD396 67759.3 453.8 0.26 14 — — — — — — CONT. — 398.3 — — 4845.8 — — 9.9 — — LYD504 67136.2 — — — 5918.8 0.02 8 10.8  0.03 3 LYD504 67140.1 383.1 0.15  6 — — — — — — LYD484 67133.3 — — — 5720.5 0.19 4 — — — LYD478 67272.3 389.4 0.20  8 — — — 10.7  0.13 2 LYD470 67125.4 391.4 0.17  9 — — — — — — LYD470 67126.7 — — — 5968.8 0.25 9 — — — LYD466 67118.1 — — — 5606.2 0.19 2 — — — LYD466 67120.2 377.5 0.17  5 — — — — — — LYD442 67103.1 380.6 0.09  6 — — — — — — LYD440 66903.1 383.1 0.15  6 6168.8 L 13  11.2  0.14 8 LYD438 66899.2 — — — 6087.5 0.23 11  11.1  0.27 6 LYD438 66900.3 379.4 0.28  5 — — — — — — LYD408 67305.6 373.8 0.24  4 — — — — — — LYD395 67080.6 — — — 5843.8 0.01 7 — — — LYD387 67317.1 389.4 0.03  8 — — — — — — LYD387 67317.4 — — — — — — 10.9  0.08 4 LYD385 66891.2 — — — 5762.5 0.04 5 — — — LYD385 66893.1 — — — 5850.0 L 7 — — — LYD375 67070.2 — — — 5818.8 0.10 6 — — — LYD375 67070.3 383.8 0.19  6 5756.2 0.18 5 — — — LYD375 67071.4 — — — 6281.2 0.18 15  — — — LYD342 67063.2 — — — 5937.5 0.11 8 — — — LYD330 67046.2 417.5 L 16 5912.5 0.17 8 11.1  0.27 6 LYD330 67050.2 — — — — — — 11.1  L 6 LYD330 67050.5 — — — — — — 10.7  0.13 2 LYD329 67277.4 373.1 0.29  3 5700.0 0.04 4 — — — LYD325 67015.4 373.1 0.29  3 — — — — — — LYD322 66884.2 — — — 5700.0 0.19 4 — — — LYD320 67043.1 — — — 5706.2 0.28 4 — — — LYD320 67044.2 — — — 5748.8 0.02 5 — — — LYD318 66983.4 409.4 0.04 14 6275.0 0.15 15  — — — LYD315 67004.4 — — — — — — 11.3  0.06 8 LYD315 67005.2 — — — 5656.2 0.25 3 — — — LYD315 67007.4 413.8 0.04 15 5875.0 0.26 7 11.3  0.06 8 LYD298 66962.3 382.0 0.20  6 — — — — — — LYD293 66957.2 — — — 5793.8 L 6 — — — LYD292 66998.3 413.1 0.11 15 6712.5 L 23  — — — LYD292 67000.1 380.6 0.09  6 6362.5 0.10 16  — — — CONT. — 360.6 — — 5474.6 — — 10.5  — — LYD471 68050.2 353.8 0.05 26 4675.0 0.10 25  — — — LYD471 68050.4 — — — 4656.2 0.15 25  9.8 0.10 4 LYD446 68109.4 — — — 4143.8 0.17 11  — — — LYD446 68110.1 — — — 3943.8 0.28 6 9.7 0.30 4 LYD446 68110.3 302.5 0.24  8 4593.8 0.10 23  — — — LYD446 68111.4 — — — — — — 9.8 0.15 4 LYD432 67959.2 — — — 3937.5 0.30 6 — — — LYD432 67960.6 — — — — — — 9.8 0.18 5 LYD422 68102.3 — — — 4537.5 0.23 22  9.7 0.16 4 LYD422 68103.3 366.9 0.29 31 4587.5 0.01 23  — — — LYD417 68043.1 315.0 0.09 12 4487.5 0.27 20  — — — LYD417 68043.3 — — — 4065.2 0.17 9 — — — LYD417 68043.5 302.5 0.28  8 — — — — — — LYD385 66891.2 305.0 0.21  9 4306.2 0.04 15  — — — LYD385 66891.3 — — — — — — 9.9 0.07 6 LYD368 67661.1 324.4 0.23 16 4050.0 0.21 9 — — — LYD364 68018.3 — — — 4137.5 0.07 11  — — — LYD364 68020.1 306.9 0.17  9 — — — — — — LYD364 68020.2 — — — — — — 9.8 0.18 5 LYD351 68129.3 — — — 4131.2 0.09 11  — — — LYD344 68123.2 — — — 4400.0 0.08 18  — — — LYD335 67557.5 — — — — — — 9.7 0.16 4 LYD330 67047.8 — — — 4156.2 0.09 11  9.7 0.16 4 LYD315 67004.4 — — — — — — 9.7 0.16 4 LYD315 67007.4 362.5 0.29 29 4312.5 0.24 16  — — — LYD309 67421.4 — — — — — — 9.8 0.18 5 LYD308 66880.2 331.2 0.03 18 4075.0 0.11 9 — — — LYD299 68114.6 — — — — — — 9.6 0.29 3 LYD299 68115.4 — — — 4331.2 0.02 16  — — — LYD299 68115.6 339.4 0.01 21 4056.3 0.28 9 — — — LYD299 68115.7 — — — 4006.2 0.17 7 — — — LYD299 68118.5 347.5 0.24 24 4537.5 L 22  — — — CONT. — 280.6 — — 3731.2 — — 9.4 — — LYD517 67221.3 508.8 0.20 10 7375.0 0.03 8 — — — LYD517 67221.5 493.8 0.09  7 7412.5 0.03 9 — — — LYD517 67222.1 503.1 0.08  9 7550.0 L 11  — — — LYD515 67151.1 517.5 0.05 12 8000.0 0.08 18  — — — LYD515 67151.4 512.5 0.12 11 7343.8 0.12 8 — — — LYD515 67151.6 — — — 7612.5 L 12  — — — LYD512 67209.1 485.0 0.16  5 7556.2 0.24 11  — — — LYD512 67211.4 509.4 0.02 11 7362.5 0.03 8 — — — LYD512 67212.2 501.2 0.04  9 7331.2 0.04 8 — — — LYD502 67342.6 490.0 0.18  6 7381.2 0.03 8 — — — LYD498 67254.3 488.8 0.11  6 7081.2 0.25 4 — — — LYD492 67364.5 512.5 0.15 11 7468.8 0.14 10  — — — LYD482 67334.1 506.9 0.03 10 7637.5 L 12  — — — LYD475 67204.2 — — — 7437.5 0.23 9 — — — LYD475 67204.4 — — — 7681.2 0.26 13  — — — LYD454 67192.5 523.8 0.01 14 7275.0 0.25 7 — — — LYD454 67193.4 — — — 7387.5 0.12 9 — — — LYD452 67106.2 545.0 0.09 18 7637.5 0.11 12  — — — LYD451 67187.7 483.1 0.24  5 7112.5 0.19 5 — — — LYD451 67188.4 534.4 0.04 16 7893.8 0.08 16  10.2  0.07 5 LYD450 67182.2 — — — 7425.0 0.25 9 — — — LYD445 67353.1 — — — 7325.0 0.08 8 — — — LYD439 67094.1 — — — — — — 10.1  0.17 4 LYD439 67096.1 — — — — — — 10.4  0.03 7 LYD415 67262.1 — — — 7781.2 L 14  — — — LYD415 67266.1 — — — 7612.5 0.27 12  — — — LYD415 67266.3 — — — 7681.2 L 13  — — — LYD415 67266.6 500.0 0.04  9 7393.8 0.22 9 — — — LYD399 67448.3 556.2 0.20 21 8118.8 L 19  10.7  0.02 10  LYD397 67322.2 482.5 0.23  5 — — — — — — LYD397 67323.2 — — — 7225.0 0.13 6 — — — LYD339 67247.3 — — — — — — 10.0  0.23 3 LYD328 67238.2 491.9 0.10  7 — — — — — — LYD328 67242.1 512.5 0.30 11 7468.8 0.02 10  — — — LYD324 67168.4 492.5 0.09  7 7143.8 0.15 5 — — — LYD323 67287.3 — — — 7087.5 0.23 4 — — — LYD323 67288.2 — — — 7662.5 0.29 13  — — — LYD321 67280.1 519.4 L 13 7356.2 0.07 8 — — — LYD321 67281.6 498.8 0.05  8 7331.2 0.29 8 — — — LYD321 67283.1 484.4 0.17  5 — — — — — — LYD321 67283.3 508.8 0.10 10 7300.0 0.25 7 — — — LYD316 67437.2 512.5 0.01 11 7412.5 0.07 9 — — — LYD316 67439.1 — — — 7356.2 0.11 8 — — — LYD312 67256.4 518.8 L 13 7868.8 L 16  — — — LYD312 67257.3 511.9 0.01 11 7293.8 0.05 7 — — — LYD310 67163.1 486.9 0.26  6 7343.8 0.04 8 — — — LYD310 67164.1 494.4 0.24  7 — — — 10.1  0.15 4 LYD309 67418.3 518.1 L 12 7737.5 0.02 14  — — — LYD296 67359.1 515.0 0.01 12 7718.8 L 13  10.1  0.17 4 LYD291 67400.2 529.1 0.17 15 7560.7 0.07 11  — — — LYD291 67400.5 — — — 7806.2 0.11 15  — — — LYD290 67233.3 — — — 7187.5 0.21 6 — — — LYD290 67233.5 — — — 7331.2 0.12 8 — — — LYD290 67236.4 — — — 7368.8 0.18 8 — — — CONT. — 460.8 — — 6804.7 — — 9.7 — — LYD489 67785.4 — — — 5331.2 L 10  — — — LYD489 67787.4 — — — 5093.8 0.22 5 — — — LYD458 67922.2 434.4 0.24  6 — — — — — — LYD453 67484.1 436.9 0.07  6 — — — — — — LYD453 67485.1 — — — — — — 10.6  0.20 4 LYD453 67487.2 — — — — — — 11.8  L 15  LYD448 67918.2 — — — 5168.8 0.16 7 10.6  0.15 4 LYD433 67700.1 — — — 5162.5 0.26 7 — — — LYD433 67704.4 — — — — — — 10.9  0.21 7 LYD409 67467.4 — — — 5193.8 0.05 7 — — — LYD409 67468.1 — — — 5300.0 0.30 10  11.4  0.08 12  LYD404 67690.2 — — — 5464.6 0.13 13  — — — LYD403 67768.3 — — — 5087.5 0.16 5 — — — LYD403 67771.1 — — — 5375.0 0.16 11  — — — LYD402 67760.2 451.5 0.02 10 5151.8 0.05 6 — — — LYD402 67762.3 — — — — — — 11.1  0.02 9 LYD402 67765.3 — — — 5168.8 0.06 7 — — — LYD368 67659.1 — — — 5520.5 0.24 14  11.1  0.27 8 LYD368 67659.5 460.6 0.23 12 — — — — — — LYD368 67661.1 — — — 5325.0 0.30 10  — — — LYD355 67640.1 — — — 5106.2 0.20 6 — — — LYD347 67844.2 — — — 5450.0 0.13 13  — — — LYD346 67605.4 — — — 5231.2 0.19 8 — — — CONT. — 411.0 — — 4839.6 — — 10.2  — — LYD483 68054.3 264.4 0.16 13 3631.2 0.12 12  — — — LYD483 68054.4 256.2 0.14  9 3487.5 0.27 8 — — — LYD483 68056.4 265.0 0.06 13 — — — — — — LYD478 67268.1 — — — — — — 9.8 0.02 5 LYD478 67269.2 265.6 0.05 13 3956.2 L 22  — — — LYD478 67270.1 — — — 3637.5 0.16 12  — — — LYD460 67930.1 286.2 L 22 — — — — — — LYD460 67930.3 — — — — — — 10.3  0.04 11  LYD423 68216.2 — — — 3600.0 0.23 11  — — — LYD423 68216.3 262.5 0.06 12 3600.0 0.10 11  — — — LYD423 68218.7 — — — 3768.8 0.03 16  — — — LYD395 67077.1 — — — 3806.2 0.14 18  — — — LYD395 67078.1 — — — — — — 9.8 0.14 6 LYD395 67080.6 — — — 3600.0 0.21 11  — — — LYD392 68032.2 257.5 0.11 10 — — — 9.6 0.13 3 LYD392 68033.3 — — — 3525.0 0.28 9 — — — LYD388 68098.3 — — — — — — 9.6 0.13 3 LYD376 68024.2 — — — 3963.4 L 22  — — — LYD376 68025.1 — — — — — — 9.6 0.06 4 LYD376 68026.2 — — — 3637.5 0.08 12  — — — LYD367 68066.5 270.0 0.18 15 3731.2 0.11 15  — — — LYD367 68066.6 — — — 3550.0 0.18 10  — — — LYD367 68068.5 257.5 0.11 10 — — — LYD365 68092.3 — — — 3556.2 0.23 10  — — — LYD365 68092.4 — — — 3518.8 0.19 9 — — — LYD365 68092.5 — — — 3525.0 0.20 9 — — — LYD361 68145.9 — — — — — — 9.6 0.13 3 LYD361 68146.7 255.0 0.14  9 3668.8 0.07 13  — — — LYD361 68147.1 — — — — — — 9.9 0.20 6 LYD360 68061.2 — — — — — — 9.8 0.14 6 LYD360 68064.1 — — — — — — 9.6 0.13 3 LYD356 68139.2 — — — 3737.5 0.04 15  9.6 0.13 3 LYD356 68140.3 — — — — — — 9.9 0.04 6 LYD354 68133.6 — — — 3712.5 0.09 15  — — — LYD349 68084.1 — — — 3562.5 0.14 10  — — — LYD349 68085.5 — — — — — — 9.5 0.20 2 LYD349 68085.6 — — — — — — 9.6 0.15 4 LYD332 66988.1 321.2 L 37 3981.2 L 23  — — — LYD332 66989.2 286.2 L 22 3700.0 0.05 14  — — — LYD325 67015.4 — — — 3506.2 0.20 8 — — — LYD297 67227.5 — — — — — — 9.8 0.14 6 CONT. — 234.6 — — 3237.5 — — 9.3 — — LYD434 67978.2 — — — — — — 9.7 0.22   3.1 LYD434 67977.3 — — — — — — 9.6 0.32   2.1 CONT. — — — — — — — 9.4 — — LYD305 67535.2 440.3 0.19 10 4865.8 0.84   1.2 — — — CONT. — 400.4 — — 4808.2 — — — — — LYD481 67778.1 471.2 0.07   18.3 — — — — — — LYD491 67874.3 428.1 0.45   7.5 — — — — — — LYD435 67709.2 420.0 0.58   5.4 — — — — — — LYD481 67779.4 420.0 0.58   5.4 — — — — — — CONT. — 398.3 — — — — — — — — Table 61. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L - p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 14467). “—” = results are still unavailable.

TABLE 62 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter Plot Coverage Rosette Area Rosette Diameter [cm²] [cm²] [cm] Gene P- % P- % P- % Name Event # Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD479 67728.5 — — — — — — 4.5 0.07 8 LYD396 67754.1 — — — — — — 4.5 0.27 6 CONT. — — — — — — — 4.2 — — LYD504 67136.2 79.9 0.03 16 10.0  0.03 16 5.5 L 10 LYD484 67135.3 — — — — — — 5.2 0.15 4 LYD478 67269.2 79.6 L 15 10.0  L 15 5.5 L 11 LYD478 67272.3 74.9 0.16  8 9.4 0.16  8 — — — LYD470 67126.7 — — — — — — 5.1 0.24 3 LYD470 67127.3 — — — — — — 5.1 0.19 3 LYD440 66903.1 75.7 0.06  9 9.5 0.06  9 5.3 L 7 LYD438 66898.3 — — — — — — 5.2 0.16 4 LYD438 66899.2 82.4 0.21 19 10.3  0.21 19 5.6 0.05 12 LYD438 66900.3 74.5 0.15  8 9.3 0.15  8 5.2 0.18 5 LYD414 67091.1 — — — — — — 5.1 0.25 2 LYD408 67305.6 74.4 0.26  8 9.3 0.26  8 — — — LYD387 67317.4 74.5 0.07  8 9.3 0.07  8 5.3 0.09 7 LYD385 66893.1 — — — — — — 5.2 0.08 4 LYD385 66893.2 — — — — — — 5.2 0.09 5 LYD342 67063.2 — — — — — — 5.2 0.05 4 LYD337 66995.4 — — — — — — 5.1 0.19 3 LYD332 66988.2 74.4 0.20  7 9.3 0.20  7 5.4 0.06 7 LYD330 67046.2 83.5 L 21 10.4  L 21 5.5 0.01 11 LYD330 67050.2 — — — — — — 5.5 0.02 10 LYD329 67277.4 74.2 0.07  7 9.3 0.07  7 5.1 0.19 3 LYD320 67040.2 — — — — — — 5.4 0.26 7 LYD318 66983.4 76.1 0.08 10 9.5 0.08 10 5.3 0.03 7 LYD315 67005.2 — — — — — — 5.2 0.25 3 LYD315 67007.1 75.7 0.09  9 9.5 0.09  9 5.3 L 7 LYD307 66975.3 — — — — — — 5.1 0.20 3 LYD307 66976.3 — — — — — — 5.2 0.09 4 CONT. — 69.2 — — 8.6 — — 5.0 — — LYD471 68050.2 48.2 0.06 21 6.0 0.06 21 4.3 0.09 6 LYD471 68050.4 47.6 0.02 19 6.0 0.02 19 4.5 0.07 10 LYD446 68109.4 45.8 0.06 15 5.7 0.06 15 4.4 L 9 LYD446 68110.3 48.1 L 20 6.0 L 20 4.3 0.10 5 LYD438 66899.2 42.4 0.20  6 5.3 0.20  6 — — — LYD432 67961.5 — — — — — — 4.2 0.22 2 LYD422 68103.3 46.3 0.18 16 5.8 0.18 16 4.2 0.25 4 LYD417 68043.3 44.3 0.04 11 5.5 0.04 11 — — — LYD385 66891.2 47.1 L 18 5.9 L 18 4.3 0.02 7 LYD385 66891.3 51.9 0.04 30 6.5 0.04 30 4.5 0.04 10 LYD368 67660.4 45.4 0.07 14 5.7 0.07 14 4.2 0.11 5 LYD364 68018.3 42.2 0.21  6 5.3 0.21  6 — — — LYD364 68020.5 49.9 0.05 25 6.2 0.05 25 4.4 0.10 9 LYD351 68126.2 48.4 0.12 21 6.1 0.12 21 4.3 0.07 6 LYD351 68129.3 45.3 0.24 13 5.7 0.24 13 4.2 0.23 3 LYD330 67047.8 43.2 0.13  8 5.4 0.13  8 4.2 0.10 4 LYD315 67004.4 43.3 0.10  8 5.4 0.10  8 — — — LYD315 67006.2 42.2 0.24  6 5.3 0.24  6 — — — LYD315 67007.4 43.6 0.09  9 5.4 0.09  9 — — — LYD299 68115.4 46.1 0.07 16 5.8 0.07 16 4.3 0.16 6 LYD299 68118.5 45.0 0.02 13 5.6 0.02 13 4.2 0.08 4 CONT. — 39.9 — — 5.0 — — 4.1 — — LYD517 67221.3 51.3 0.17 16 6.4 0.17 16 4.5 0.23 8 LYD517 67221.5 54.1 0.02 22 6.8 0.02 22 4.8 L 15 LYD517 67222.1 53.1 0.21 20 6.6 0.21 20 4.6 0.11 10 LYD515 67151.1 61.3 L 39 7.7 L 39 5.0 L 21 LYD515 67151.6 — — — — — — 4.4 0.19 6 LYD515 67152.4 — — — — — — 4.5 0.17 8 LYD512 67209.1 49.2 0.14 11 6.2 0.14 11 4.5 0.10 8 LYD512 67212.2 56.4 0.05 27 7.0 0.05 27 4.8 0.15 15 LYD502 67342.6 53.2 0.05 20 6.7 0.05 20 4.6 0.04 11 LYD498 67254.3 49.2 0.19 11 6.2 0.19 11 — — — LYD482 67334.1 55.2 0.15 25 6.9 0.15 25 4.7 0.16 14 LYD475 67204.2 48.0 0.28  8 6.0 0.28  8 4.5 0.14 9 LYD454 67193.4 54.9 0.13 24 6.9 0.13 24 4.6 0.05 11 LYD452 67106.1 47.7 0.29  8 6.0 0.29  8 4.4 0.14 7 LYD452 67106.2 52.5 0.05 19 6.6 0.05 19 4.6 0.03 11 LYD452 67106.4 — — — — — — 4.4 0.15 7 LYD452 67108.1 48.2 0.30  9 6.0 0.30  9 4.3 0.28 5 LYD451 67187.7 51.3 0.20 16 6.4 0.20 16 4.7 0.22 12 LYD451 67188.4 52.6 0.02 19 6.6 0.02 19 4.6 0.04 11 LYD450 67182.2 51.4 0.11 16 6.4 0.11 16 4.5 0.11 9 LYD445 67352.3 — — — — — — 4.5 0.23 8 LYD439 67094.1 50.3 0.19 14 6.3 0.19 14 4.5 0.08 10 LYD439 67096.1 61.0 0.16 38 7.6 0.16 38 4.9 0.11 19 LYD415 67262.1 58.2 L 31 7.3 L 31 4.9 L 18 LYD415 67264.5 49.1 0.22 11 6.1 0.22 11 4.4 0.20 6 LYD415 67266.3 55.6 L 26 7.0 L 26 4.8 0.01 15 LYD415 67266.6 51.7 0.04 17 6.5 0.04 17 4.6 0.07 10 LYD399 67448.3 63.9 L 44 8.0 L 44 5.1 L 23 LYD339 67247.3 54.4 0.01 23 6.8 0.01 23 4.8 L 16 LYD328 67242.1 53.5 0.03 21 6.7 0.03 21 4.7 0.05 12 LYD324 67168.4 49.9 0.15 13 6.2 0.15 13 4.4 0.11 7 LYD323 67287.1 — — — — — — 4.7 0.26 14 LYD323 67288.2 57.9 0.04 31 7.2 0.04 31 4.7 0.05 14 LYD321 67280.1 58.2 0.09 31 7.3 0.09 31 4.8 0.17 15 LYD321 67281.6 52.6 0.27 19 6.6 0.27 19 — — — LYD321 67283.1 54.3 0.11 23 6.8 0.11 23 4.7 0.10 13 LYD316 67439.1 49.5 0.12 12 6.2 0.12 12 4.4 0.21 5 LYD312 67256.3 49.3 0.14 11 6.2 0.14 11 4.3 0.25 5 LYD312 67256.4 57.2 0.09 29 7.2 0.09 29 4.7 0.18 14 LYD312 67257.3 52.2 0.05 18 6.5 0.05 18 4.6 0.02 12 LYD310 67163.1 53.5 0.06 21 6.7 0.06 21 4.7 0.01 14 LYD309 67418.1 — — — — — — 4.4 0.22 6 LYD309 67418.3 52.8 0.04 19 6.6 0.04 19 4.5 0.06 9 LYD309 67420.1 47.7 0.29  8 6.0 0.29  8 4.3 0.25 5 LYD296 67359.1 61.2 L 38 7.7 L 38 5.0 L 21 LYD296 67359.3 63.9 0.13 44 8.0 0.13 44 5.2 0.02 26 LYD291 67400.2 47.9 0.25  8 6.0 0.25  8 4.4 0.12 7 LYD291 67400.5 55.9 L 26 7.0 L 26 4.7 L 13 LYD291 67401.4 53.5 0.02 21 6.7 0.02 21 4.7 L 13 LYD290 67233.3 — — — — — — 4.4 0.17 7 LYD290 67236.4 — — — — — — 4.4 0.29 6 CONT. — 44.3 — — 5.5 — — 4.1 — — LYD501 67889.1 — — — — — — 4.9 0.07 8 LYD489 67787.3 — — — — — — 4.9 0.22 7 LYD453 67487.2 70.8 0.08 18 8.8 0.08 18 5.0 0.25 10 LYD448 67918.2 70.5 0.02 18 8.8 0.02 18 5.0 0.02 10 LYD409 67468.1 73.2 L 22 9.2 L 22 4.9 0.05 9 LYD403 67770.3 67.0 0.22 12 8.4 0.22 12 — — — LYD402 67762.3 78.1 L 30 9.8 L 30 5.3 L 16 LYD368 67659.1 74.3 0.27 24 9.3 0.27 24 5.0 0.19 11 LYD347 67844.2 71.5 0.23 19 8.9 0.23 19 5.0 0.19 9 LYD347 67845.1 — — — — — — 4.9 0.23 7 LYD347 67847.3 — — — — — — 4.9 0.27 7 LYD346 67605.4 74.1 L 24 9.3 L 24 5.1 L 13 LYD346 67606.2 — — — — — — 5.0 0.02 10 CONT. — 59.9 — — 7.5 — — 4.6 — — LYD483 68054.1 — — — — — — 3.8 0.25 4 LYD483 68054.4 — — — — — — 3.8 0.21 4 LYD483 68056.4 36.5 0.22  9 4.6 0.22  9 3.9 0.25 6 LYD483 68056.5 36.2 L  8 4.5 L  8 3.9 0.01 8 LYD478 67269.2 37.7 0.08 12 4.7 0.08 12 4.0 L 9 LYD478 67270.1 39.6 0.10 18 4.9 0.10 18 4.0 0.03 9 LYD423 68216.2 41.1 0.17 22 5.1 0.17 22 4.1 0.21 13 LYD423 68218.7 38.9 L 16 4.9 L 16 4.0 0.16 10 LYD395 67077.1 39.0 L 16 4.9 L 16 4.0 L 10 LYD395 67080.6 38.9 L 16 4.9 L 16 3.9 0.22 7 LYD392 68030.1 38.4 L 14 4.8 L 14 4.0 L 9 LYD392 68032.2 — — — — — — 4.1 0.16 13 LYD392 68033.3 44.4 0.13 32 5.6 0.13 32 4.2 0.14 16 LYD392 68035.1 — — — — — — 3.9 0.18 8 LYD388 68096.5 — — — — — — 3.8 0.03 3 LYD388 68098.4 — — — — — — 3.9 0.20 7 LYD376 68024.2 41.1 0.23 22 5.1 0.23 22 4.1 0.23 12 LYD376 68026.2 36.7 0.08  9 4.6 0.08  9 4.0 L 8 LYD367 68066.1 — — — — — — 3.9 0.08 7 LYD367 68066.5 36.8 0.01 10 4.6 0.01 10 4.0 L 9 LYD367 68068.5 36.3 0.07  8 4.5 0.07  8 — — — LYD365 68092.3 35.3 0.24  5 4.4 0.24  5 3.8 0.10 4 LYD365 68092.4 40.4 L 20 5.1 L 20 4.0 0.01 10 LYD365 68092.5 — — — — — — 3.9 0.03 6 LYD361 68146.7 40.3 0.10 20 5.0 0.10 20 4.1 0.08 11 LYD360 68061.2 42.2 0.06 26 5.3 0.06 26 4.1 0.12 11 LYD360 68064.1 — — — — — — 3.7 0.11 3 LYD356 68139.2 39.9 0.11 19 5.0 0.11 19 4.0 0.16 9 LYD356 68142.2 — — — — — — 3.8 0.07 4 LYD354 68133.6 40.8 0.01 21 5.1 0.01 21 4.1 L 12 LYD354 68133.9 — — — — — — 3.8 0.05 3 LYD354 68134.1 — — — — — — 3.7 0.13 2 LYD349 68084.1 36.3 0.26  8 4.5 0.26  8 3.9 0.26 5 LYD349 68085.3 40.7 0.03 21 5.1 0.03 21 4.0 L 9 LYD332 66988.1 41.2 L 22 5.1 L 22 4.2 L 14 LYD332 66988.2 — — — — — — 3.9 0.16 7 LYD332 66989.2 — — — — — — 3.9 0.24 8 LYD325 67013.2 — — — — — — 3.8 0.09 5 CONT. — 33.6 — — 4.2 — — 3.7 — — Table 62. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L - p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 14467). “—” = results are still unavailable.

TABLE 63 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter RGR Of RGR Of RGR Of Rosette Leaf Number Plot Coverage Diameter Gene P- % P- % P- % Name Event # Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD496 67741.5 0.8 0.25 14 — — — — — — LYD479 67728.5 — — — — — — 0.4 0.27 10 LYD396 67754.1 — — — 7.2 0.25 16 — — — CONT. — 0.7 — — 6.2 — — 0.4 — — LYD504 67136.2 — — — 10.1  0.15 16 0.5 0.15  9 LYD484 67133.3 0.8 0.10 12 — — — — — — LYD484 67135.3 — — — — — — 0.5 0.29  7 LYD478 67269.2 — — — 10.2  0.11 17 0.5 0.02 15 LYD466 67118.1 0.9 0.01 23 — — — 0.5 0.30  7 LYD440 66903.1 0.8 0.03 16 9.7 0.29 11 0.5 0.20  8 LYD438 66899.2 — — — 10.5  0.07 20 0.5 0.04 14 LYD387 67317.4 0.8 0.13 11 — — — 0.5 0.11 11 LYD385 66893.1 — — — — — — 0.5 0.28  7 LYD375 67071.4 — — — — — — 0.5 0.21  9 LYD342 67063.2 — — — — — — 0.5 0.24  7 LYD334 67294.3 0.8 0.03 17 — — — — — — LYD332 66988.2 — — — — — — 0.5 0.22  8 LYD330 67046.2 — — — 10.5  0.06 20 0.5 0.07 12 LYD330 67050.2 0.8 0.25  9 10.1  0.16 16 0.5 0.06 12 LYD330 67050.5 0.8 0.20  9 — — — — — — LYD318 66983.4 — — — — — — 0.5 0.07 12 LYD315 67004.4 0.8 0.04 15 — — — — — — LYD315 67007.1 0.8 0.07 15 — — — — — — LYD315 67007.4 0.8 0.12 13 — — — 0.5 0.24  8 LYD307 66976.3 0.8 0.12 11 — — — 0.5 0.20  8 LYD292 66998.3 — — — 10.0  0.18 15 — — — CONT. — 0.7 — — 8.7 — — 0.4 — — LYD471 68050.2 — — — 6.2 0.14 22 — — — LYD471 68050.4 — — — 6.0 0.19 19 — — — LYD446 68110.3 — — — 6.2 0.15 22 — — — LYD422 68102.3 — — — 6.1 0.17 22 — — — LYD422 68103.3 — — — 5.9 0.26 17 — — — LYD417 68043.1 — — — 5.9 0.28 17 — — — LYD385 66891.3 — — — 6.6 0.04 32 — — — LYD364 68020.5 — — — 6.4 0.09 26 — — — LYD351 68126.2 — — — 6.1 0.19 20 — — — LYD330 67046.2 — — — 6.0 0.22 19 — — — LYD309 67421.4 0.7 0.16 21 — — — — — — CONT. — 0.6 — — 5.0 — — — — — LYD517 67221.5 — — — 6.9 0.16 22 0.4 0.15 19 LYD517 67222.1 — — — 6.8 0.20 21 — — — LYD515 67151.1 — — — 7.9 0.02 39 0.4 0.07 24 LYD512 67212.2 — — — 7.2 0.10 27 0.4 0.21 16 LYD502 67342.6 — — — 6.8 0.20 20 — — — LYD482 67334.1 — — — 7.1 0.13 25 0.4 0.14 19 LYD475 67204.2 — — — — — — 0.4 0.20 16 LYD475 67204.4 — — — 7.1 0.14 25 0.4 0.30 15 LYD454 67193.4 — — — 7.1 0.13 25 0.4 0.30 13 LYD452 67106.2 — — — 6.7 0.25 18 — — — LYD451 67188.4 — — — 6.7 0.26 18 — — — LYD439 67096.1 — — — 7.8 0.03 38 0.4 0.15 19 LYD415 67262.1 — — — 7.5 0.06 31 0.4 0.11 20 LYD415 67266.3 — — — 7.1 0.11 26 0.4 0.19 17 LYD399 67448.3 — — — 8.3 L 46 0.5 0.04 28 LYD339 67247.3 — — — 7.0 0.14 24 0.4 0.10 21 LYD328 67242.1 — — — 6.9 0.17 22 0.4 0.15 18 LYD323 67287.1 — — — 7.1 0.15 24 0.4 0.26 15 LYD323 67288.2 — — — 7.4 0.06 31 0.4 0.25 15 LYD321 67280.1 — — — 7.5 0.05 33 0.4 0.16 18 LYD321 67281.6 — — — 6.7 0.25 19 — — — LYD321 67283.1 — — — 6.9 0.17 22 — — — LYD316 67437.2 — — — 6.8 0.25 20 — — — LYD312 67256.4 — — — 7.3 0.07 29 0.4 0.26 15 LYD312 67257.3 — — — 6.6 0.29 17 — — — LYD310 67163.1 — — — 6.8 0.21 20 0.4 0.26 15 LYD309 67418.3 — — — 6.7 0.24 19 — — — LYD296 67359.1 — — — 7.9 0.02 39 0.5 0.05 25 LYD296 67359.3 — — — 8.1 0.01 44 0.5 0.03 29 LYD291 67400.5 — — — 7.1 0.11 26 0.4 0.23 15 LYD291 67401.4 — — — 6.9 0.19 21 0.4 0.22 16 CONT. — — — — 5.7 — — 0.4 — — LYD453 67487.2 0.8 0.18 17 8.8 0.14 17 — — — LYD448 67918.2 — — — 8.9 0.12 17 — — — LYD409 67468.1 — — — 9.0 0.09 19 — — — LYD403 67770.3 — — — 8.5 0.28 13 — — — LYD402 67762.1 — — — 8.8 0.27 17 — — — LYD402 67762.3 — — — 9.6 0.03 27 — — — LYD368 67659.1 — — — 9.3 0.06 23 — — — LYD347 67844.2 — — — 8.9 0.13 18 — — — LYD346 67605.4 — — — 9.2 0.06 22 0.5 0.18 12 CONT. — 0.7 — — 7.5 — — 0.4 — — LYD478 67270.1 — — — 4.9 0.24 17 — — — LYD460 67930.3 0.8 0.03 36 — — — — — — LYD460 67931.2 0.6 0.28 16 — — — — — — LYD423 68216.2 — — — 5.2 0.11 24 0.4 0.18 14 LYD423 68218.3 0.7 0.21 20 — — — — — — LYD423 68218.7 — — — 4.9 0.24 17 0.3 0.23 12 LYD395 67077.1 — — — 4.9 0.23 17 0.3 0.26 11 LYD395 67080.6 — — — 4.9 0.25 16 — — — LYD392 68032.2 — — — 4.9 0.25 17 0.4 0.17 14 LYD392 68033.3 — — — 5.5 0.05 31 0.4 0.17 15 LYD392 68035.1 — — — — — — 0.3 0.27 11 LYD376 68024.2 — — — 5.2 0.14 22 0.4 0.19 14 LYD376 68025.3 0.6 0.25 17 — — — — — — LYD376 68026.2 — — — — — — 0.3 0.26 11 LYD367 68066.5 — — — — — — 0.3 0.24 13 LYD365 68092.4 — — — 5.1 0.14 21 0.3 0.24 11 LYD361 68146.5 — — — 4.9 0.28 16 — — — LYD361 68146.7 — — — 5.1 0.14 21 0.3 0.22 12 LYD360 68061.2 — — — 5.3 0.10 25 — — — LYD360 68063.2 0.7 0.28 18 — — — — — — LYD356 68139.2 — — — 5.0 0.21 18 — — — LYD356 68142.2 0.7 0.20 20 — — — — — — LYD354 68133.6 — — — 5.2 0.13 22 0.3 0.23 12 LYD349 68085.3 — — — 5.1 0.15 21 — — — LYD332 66988.1 — — — 5.2 0.12 23 0.4 0.10 17 LYD332 66989.2 — — — 4.9 0.27 16 — — — CONT. — 0.6 — — 4.2 — — 0.3 — — Table 63. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L - p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 14467). “—” = results are still unavailable.

TABLE 64 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter Petiole Relative Petiole Relative Petiole Relative Area TP2 Area TP3 Area TP4 Gene P- P- % P- % Name Event # Ave. Val. % Incr. Ave. Val. Incr. Ave. Val. Incr. LYD520 67310.2 11.6 0.068 14.9 14.2 0.53 2.9 LYD520 67310.1 11.6 0.074 14.3 LYD520 67310.3 11.5 0.076 14.0 LYD520 67313.3 11.5 0.078 13.9 LYD520 67312.1 11.5 0.085 13.2 LYD519 67156.2 10.8 0.42 6.9 LYD519 67157.2 10.7 0.43 6.5 LYD519 67154.3 10.7 0.44 6.3 Table 64. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L - p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 14467). “TP” = a relative time point between measurements. “—” = results are still unavailable.

Example 18 Evaluating Transgenic Arabidopsis Under Normal Conditions Using In Vitro Assays [Tissue Culture T2 and T1 Plants, TC-T2 and TC-T1 Assays]

Surface sterilized seeds were sown in basal media [50% Murashige-Skoog medium (MS) supplemented with 0.8% plant agar as solidifying agent] in the presence of Kanamycin (used as a selecting agent). After sowing, plates were transferred for 2-3 days for stratification at 4° C. and then grown at 25° C. under 12-hour light 12-hour dark daily cycles for 7 to 10 days. At this time point, seedlings randomly chosen were carefully transferred to plates containing ½ MS media (15 mM N). For experiments performed in T₂ lines, each plate contained 5 seedlings of the same transgenic event, and 3-4 different plates (replicates) for each event. For each polynucleotide of the invention at least four-five independent transformation events were analyzed from each construct. For experiments performed in T₁ lines, each plate contained 5 seedlings of 5 independent transgenic events and 3-4 different plates (replicates) were planted. In total, for T₁ lines, 20 independent events were evaluated. Plants expressing the polynucleotides of the invention were compared to the average measurement of the control plants (empty vector or GUS reporter gene under the same promoter) used in the same experiment.

Digital imaging—A laboratory image acquisition system, which consists of a digital reflex camera (Canon EOS 300D) attached with a 55 mm focal length lens (Canon EF-S series), mounted on a reproduction device (Kaiser RS), which includes 4 light units (4×150 Watts light bulb) and located in a darkroom, was used for capturing images of plantlets sawn in agar plates.

The image capturing process was repeated every 3-4 days starting at day 1 till day 10 (see for example the images in FIGS. 3A-3F). An image analysis system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program—ImageJ 1.39 [Java based image processing program which was developed at the U.S. National Institutes of Health and freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Images were captured in resolution of 10 Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute).

Seedling analysis—Using the digital analysis seedling data was calculated, including leaf area, root coverage and root length.

The relative growth rate for the various seedling parameters was calculated according to the following formulas XIV (RGR leaf area), and XV (RGR root length).

Relative growth rate of leaf area=Regression coefficient of leaf area along time course.  Formula XIV:

Relative growth rate of root length=Regression coefficient of root length along time course.  Formula XV:

At the end of the experiment, plantlets were removed from the media and weighed for the determination of plant fresh weight. Plantlets were then dried for 24 hours at 60° C., and weighed again to measure plant dry weight for later statistical analysis. The fresh and dry weights are provided for each Arabidopsis plant. Growth rate was determined by comparing the leaf area coverage, root coverage and root length, between each couple of sequential photographs, and results were used to resolve the effect of the gene introduced on plant vigor under optimal conditions. Similarly, the effect of the gene introduced on biomass accumulation, under optimal conditions, was determined by comparing the plants' fresh and dry weight to that of control plants (containing an empty vector or the GUS reporter gene under the same promoter). From every construct created, 3-5 independent transformation events were examined in replicates.

Statistical analyses—To identify genes conferring significantly improved plant vigor or enlarged root architecture, the results obtained from the transgenic plants were compared to those obtained from control plants. To identify outperforming genes and constructs, results from the independent transformation events tested were analyzed separately. To evaluate the effect of a gene event over a control the data was analyzed by Student's t-test and the p value was calculated. Results were considered significant if p<0.1. The JMP statistics software package was used (Version 5.2.1, SAS Institute Inc., Cary, N.C., USA).

Experimental Results

Tables 65-67 summarize the observed phenotypes of transgenic plants expressing the gene constructs using the TC-T2 Assays.

The genes presented in Table 65 showed a significant improvement as they produced larger plant biomass (plant fresh and dry weight) in T2 generation when grown under normal growth conditions, compared to control plants. The genes were cloned under the regulation of a constitutive promoter (At6669, SEQ ID NO:14467).

The evaluation of each gene was carried out by testing the performance of different number of events. Some of the genes were evaluated in more than one tissue culture assay. The results obtained in these second experiments were significantly positive as well.

TABLE 65 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter Gene Dry Weight [mg] Fresh Weight [mg] Name Event # Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD480 68333.4 11.6 0.02 88 223.1 0.03 95 LYD477 68234.4 10.0 0.16 62 194.1 0.12 70 LYD477 68237.2  8.6 0.14 39 170.6 0.06 49 LYD470 67126.7 10.0 0.06 62 181.5 0.04 59 LYD420 68342.1 14.1 0.02 128  242.3 0.02 112  LYD419 67911.3 11.7 0.11 90 216.0 0.11 89 LYD418 68336.1  8.1 0.25 32 — — — LYD398 68038.2  8.0 0.29 29 152.2 0.21 33 LYD377 67952.3  8.1 0.29 31 — — — LYD358 68274.1 — — — 158.3 0.22 39 LYD352 68328.3  8.8 0.25 43 160.3 0.18 40 CONT. —  6.2 — — 114.3 — — LYD507 67552.3 14.5 L 133  276.8 L 125  LYD507 67552.5  9.8 0.10 57 180.2 0.16 47 LYD507 67553.4 10.3 0.28 65 209.9 0.24 71 LYD487 67498.1 — — — 156.7 0.24 27 LYD487 67498.3  9.8 0.02 58 212.8 0.02 73 LYD487 67500.1  9.4 0.26 51 186.9 0.20 52 LYD473 67493.1  8.9 0.24 43 175.0 0.29 42 LYD473 67494.1  8.6 0.18 38 169.2 0.26 38 LYD465 67569.2  9.6 0.03 55 189.4 0.01 54 LYD461 67522.6  9.3 0.23 49 196.8 0.21 60 LYD449 67479.1  8.9 0.06 44 181.7 0.10 48 LYD449 67482.2  8.1 0.30 30 — — — LYD393 67563.1 11.4 0.09 82 214.9 0.09 75 LYD331 67592.1 11.7 0.10 88 221.7 0.08 80 LYD331 67593.1 10.5 0.01 69 197.5 0.03 61 LYD327 67589.5 11.6 0.09 86 204.0 0.06 66 LYD313 67430.1  8.6 0.29 37 — — — LYD313 67432.1 11.9 0.09 91 223.8 0.10 82 LYD294 67406.1 13.1 0.03 110  274.1 0.04 123  LYD294 67407.4  8.8 0.14 41 167.2 0.21 36 LYD289 67461.4  9.2 0.23 48 206.1 0.13 68 CONT. —  6.2 — — 122.9 — — LYD477 68234.1 14.1 0.12 55 270.7 0.07 77 LYD377 67952.4 12.3 0.05 35 201.3 0.08 32 LYD359 67947.2 14.9 0.02 63 257.8 L 69 LYD343 67067.3 14.8 L 62 269.9 L 77 LYD343 67068.6 — — — 210.3 0.26 38 LYD319 67833.3 10.5 0.24 15 — — — LYD295 67971.5 15.4 0.03 69 253.8 0.03 66 CONT. —  9.1 — — 152.8 — — LYD507 67552.2 14.1 L 140  268.5 L 144  LYD507 67552.3 11.8 0.02 101  204.2 0.06 85 LYD507 67553.5 10.3 L 76 188.6 L 71 LYD487 67496.1  7.3 0.26 25 — — — LYD473 67493.1 11.2 0.03 91 195.3 0.02 77 LYD393 67562.3  7.6 0.28 29 — — — LYD393 67563.5 10.0 0.17 71 183.9 0.22 67 LYD390 67684.3  7.9 0.19 35 142.8 0.18 30 LYD390 67686.2  9.7 0.11 64 176.7 0.05 60 LYD370 67665.2  8.0 0.25 36 — — — LYD370 67666.2 13.1 0.06 122  244.0 0.05 121  LYD340 67600.3  8.3 0.20 41 141.1 0.24 28 LYD340 67600.5 10.2 0.05 74 169.2 0.11 54 LYD340 67601.3 13.4 L 128  255.6 L 132  LYD331 67593.5  8.3 0.16 42 158.7 0.09 44 LYD331 67594.1  9.4 0.26 60 — — — LYD331 67594.3  7.5 0.24 28 142.8 0.16 30 LYD327 67588.1 — — — 167.5 0.24 52 LYD327 67589.5 10.3 0.11 75 189.2 0.07 72 LYD327 67589.6 10.3 0.03 75 204.8 0.08 86 LYD313 67432.1  9.2 0.08 56 161.1 0.15 46 LYD294 67407.6  8.2 0.17 40 144.1 0.29 31 CONT. —  5.9 — — 110.2 — — LYD518 67750.1 15.4 0.05 57 241.9 0.22 27 LYD516 67743.4 16.0 0.19 63 277.8 0.24 45 LYD516 67744.2 12.8 0.12 30 250.6 0.10 31 LYD516 67745.4 11.7 0.24 19 — — — LYD514 67511.4 15.9 0.02 61 278.0 0.03 46 LYD510 67828.2 19.2 L 95 341.3 L 79 LYD510 67829.1 18.4 L 87 304.9 0.04 60 LYD505 67502.1 15.2 L 54 268.8 0.04 41 LYD505 67505.2 14.6 0.17 48 262.1 0.22 37 LYD505 67507.2 14.1 0.05 43 245.7 0.26 29 LYD469 67937.2 12.1 0.19 23 — — — LYD462 67868.3 19.1 L 93 337.3 L 77 LYD462 67870.1 17.3 L 76 298.7 0.01 56 LYD462 67871.3 16.1 0.14 64 276.5 0.17 45 LYD462 67872.2 16.5 L 68 307.1 0.02 61 LYD455 67816.3 13.1 0.12 33 — — — LYD455 67817.1 12.4 0.29 26 — — — LYD424 67797.2 15.6 0.12 58 270.6 0.18 42 LYD424 67798.5 13.1 0.24 33 — — — LYD419 67913.2 12.6 0.08 28 231.2 0.25 21 LYD326 67842.3 14.5 0.15 47 289.7 0.25 52 LYD304 67806.2 15.5 0.06 57 274.3 0.13 44 CONT. —  9.8 — — 191.1 — — LYD518 67750.1  7.6 0.03 45 149.3 0.06 35 LYD516 67743.4 10.6 L 101  224.0 L 103  LYD514 67508.2  8.1 0.09 54 162.0 0.06 47 LYD514 67511.2 10.2 0.03 95 208.6 L 89 LYD514 67511.4  7.8 0.20 48 163.8 0.10 49 LYD510 67829.5  9.0 0.02 71 181.5 L 65 LYD505 67505.3 11.2 L 112  204.8 0.02 86 LYD505 67507.1  8.7 0.11 66 186.7 0.07 69 LYD469 67934.3  8.9 0.03 70 172.6 0.07 57 LYD469 67935.3  9.0 0.10 71 182.8 0.08 66 LYD469 67936.3  6.3 0.20 21 133.8 0.08 21 LYD469 67937.2  6.6 0.28 27 — — — LYD462 67868.3  6.7 0.11 27 143.0 0.06 30 LYD462 67872.2 14.1 L 169  285.9 L 159  LYD455 67818.5  8.6 0.08 63 172.6 0.13 57 LYD437 67899.1  7.2 0.17 38 156.8 0.04 42 LYD437 67899.4 10.0 0.07 90 205.9 0.08 87 LYD437 67900.1 11.5 0.01 120  214.7 0.04 95 LYD437 67900.2  8.4 0.21 60 181.7 0.15 65 LYD437 67902.5  9.8 0.02 88 224.6 0.03 104  LYD424 67798.5  7.7 0.11 47 145.4 0.15 32 LYD424 67798.6  8.0 0.10 52 160.6 0.04 46 LYD424 67799.5 10.6 L 101  218.0 L 98 LYD326 67838.1 — — — 127.4 0.18 16 LYD326 67839.4 10.4 L 98 202.5 L 84 LYD326 67840.1  6.6 0.15 25 — — — LYD304 67805.1  6.5 0.22 23 — — — LYD304 67806.1 11.2 0.03 112  234.1 0.01 112  LYD304 67806.2 13.1 0.01 150  256.8 L 133  CONT. —  5.2 — — 110.2 — — Table 65. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L - p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 14467). “—” = results are still unavailable.

The genes presented in Tables 66 and 67 show a significant improvement in plant performance since they produced a larger leaf biomass (leaf area) and root biomass (root length and root coverage) (Table 66) and a higher relative growth rate of leaf area, root coverage and root length (Table 67) when grown under normal growth conditions, compared to control plants. Plants producing larger root biomass have better possibilities to absorb larger amount of nitrogen from soil. Plants producing larger leaf biomass have better ability to produce assimilates. The genes were cloned under the regulation of a constitutive promoter (At6669). The evaluation of each gene was performed by testing the performance of different number of events. Some of the genes were evaluated in more than one tissue culture assay. This second experiment confirmed the significant increment in leaf and root performance. Event with p-value<0.1 was considered statistically significant.

TABLE 66 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter Leaf Area Roots Coverage Roots Length [cm²] [cm²] [cm] Gene P- % P- % P- % Name Event # Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD480 68331.4 — — — — — — 6.6 0.18  9 LYD480 68331.6 — — — — — — 6.7 0.11 11 LYD480 68333.4 0.8 L 58 11.3 0.08 67 6.8 0.23 12 LYD480 68335.1 — — — — — — 6.7 0.21 10 LYD477 68234.1 — — — — — — 6.9 0.06 13 LYD477 68234.4 0.8 0.07 56  9.8 0.20 45 6.8 0.23 12 LYD477 68237.1 0.7 0.05 31  9.3 0.11 39 7.1 0.02 17 LYD477 68237.2 0.7 0.02 37 — — — — — — LYD470 67126.7 0.7 0.01 46 — — — — — — LYD420 68342.1 0.9 0.01 72 13.3 0.02 98 6.8 0.20 13 LYD420 68343.2 0.6 0.10 26 — — — — — — LYD420 68344.2 — — — — — — 6.6 0.24  9 LYD419 67911.3 0.7 0.13 45 11.2 0.20 66 — — — LYD418 68336.1 0.6 0.10 25  9.5 0.09 41 7.1 0.05 17 LYD398 68037.1 — — — — — — 6.7 0.10 11 LYD398 68038.2 0.6 0.11 24  9.5 0.10 40 6.8 0.14 11 LYD398 68038.6 — — — — — — 6.7 0.15 10 LYD377 67952.3 0.7 0.06 35  9.0 0.17 34 — — — LYD377 67952.4 0.7 0.09 30 — — — 7.0 0.02 16 LYD377 67953.3 — — — — — — 6.9 0.10 13 LYD358 68274.1 0.6 0.30 21  9.0 0.24 33 6.6 0.27  9 LYD352 68327.3 — — — — — — 6.8 0.08 12 LYD352 68328.3 0.7 0.08 29 — — — — — — LYD319 67833.3 0.6 0.16 21 — — — — — — LYD509 6.1 0.89  2 CONT. — 0.5 — —  6.7 — — 6.1 — — LYD507 67552.3 1.1 L 85 13.3 L 44 7.9 0.16  5 LYD507 67552.5 0.8 0.09 33 — — — — — — LYD507 67553.4 0.8 0.15 37 — — — 7.9 0.26  5 LYD487 67498.3 0.8 0.02 34 11.1 0.14 20 — — — LYD487 67500.1 0.8 0.13 31 11.4 0.13 24 8.0 0.06  6 LYD473 67494.1 0.8 0.07 27 — — — — — — LYD465 67569.2 0.8 0.04 27 — — — — — — LYD461 67522.6 0.8 0.18 27 — — — — — — LYD449 67479.1 0.8 0.14 24 — — — — — — LYD393 67563.1 0.8 0.07 37 12.7 0.10 38 8.1 0.19  8 LYD370 67666.2 0.7 0.28 20 — — — — — — LYD331 67592.1 0.8 0.10 34 — — — — — — LYD331 67593.1 0.8 0.10 27 — — — — — — LYD327 67589.5 0.8 0.07 36 11.3 0.29 22 — — — LYD313 67430.1 0.8 0.20 22 — — — — — — LYD313 67432.1 0.9 0.10 47 14.3 0.12 55 8.4 0.09 12 LYD294 67406.1 0.9 0.03 48 11.9 0.18 29 — — — LYD294 67407.4 0.8 0.05 28 — — — — — — LYD289 67461.4 0.9 0.06 38 12.0 0.09 31 7.9 0.21  4 CONT. — 0.6 — —  9.2 — — 7.5 — — LYD477 68234.1 1.0 0.07 34 15.3 0.08 37 8.1 0.06  6 LYD456 67966.3 — — — 13.3 0.20 20 — — — LYD436 68073.1 — — — — — — 8.0 0.19  5 LYD377 67952.4 1.0 0.01 31 — — — — — — LYD359 67947.2 1.0 L 39 13.9 0.06 25 — — — LYD359 67947.4 0.9 0.18 23 — — — — — — LYD343 67064.3 0.8 0.19 14 — — — — — — LYD343 67066.2 — — — 15.4 0.08 38 8.6 L 13 LYD343 67067.3 1.1 L 44 17.4 L 57 8.2 0.09  8 LYD319 67833.3 0.9 L 29 — — — — — — LYD295 67971.5 1.1 L 52 15.6 0.06 40 8.2 0.03  8 CONT. — 0.7 — — 11.1 — — 7.6 — — LYD507 67552.2 1.1 L 95 14.4 0.02 67 7.8 0.09 10 LYD507 67552.3 0.9 0.01 55 13.0 L 50 7.9 0.03 11 LYD507 67553.5 0.8 0.01 45 11.6 0.02 35 — — — LYD473 67493.1 0.8 0.02 42 12.6 0.06 46 7.7 0.12  8 LYD473 67494.1 — — — 10.5 0.15 21 — — — LYD465 67569.2 — — — 10.7 0.18 24 7.9 0.11 10 LYD461 67520.5 — — — — — — 7.5 0.24  5 LYD461 67522.1 — — — — — — 7.8 0.05 10 LYD461 67522.2 0.7 0.22 19 10.6 0.20 23 7.6 0.23  7 LYD393 67563.5 0.8 0.20 33 — — — — — — LYD390 67683.5 — — — 10.5 0.17 22 7.6 0.27  7 LYD390 67684.3 0.7 0.19 26 10.8 0.23 26 — — — LYD390 67686.2 0.8 0.03 44 12.7 0.03 47 7.6 0.17  7 LYD370 67665.2 — — — 10.2 0.20 19 7.6 0.28  6 LYD370 67666.2 1.0 0.03 78 11.8 0.06 36 — — — LYD370 67667.1 — — — — — — 7.5 0.24  5 LYD370 67667.4 — — — — — — 7.6 0.19  7 LYD340 67600.3 0.7 0.24 21 — — — — — — LYD340 67600.5 0.7 0.16 29 — — — — — — LYD340 67601.3 1.0 L 66 13.3 L 55 7.8 0.12 10 LYD331 67593.5 0.7 0.20 19 11.4 0.03 32 7.8 0.11  9 LYD331 67594.3 — — — 10.2 0.18 19 7.6 0.17  6 LYD327 67587.4 0.7 0.08 25 — — — — — — LYD327 67588.1 0.8 0.17 44 13.6 0.12 57 8.1 0.11 13 LYD327 67588.2 0.7 0.27 16 10.0 0.26 16 — — — LYD327 67589.5 0.8 0.02 47 10.7 0.17 25 — — — LYD327 67589.6 0.8 0.02 40 11.1 0.12 28 — — — LYD313 67432.1 0.7 0.18 28 11.6 0.13 35 — — — LYD294 67407.6 — — — 12.5 0.04 45 7.7 0.10  8 LYD289 67461.1 — — — 10.0 0.28 16 — — — LYD289 67461.4 — — — — — — 7.8 0.08  9 CONT. — 0.6 — —  8.6 — — 7.1 — — LYD518 67748.2 — — — 15.1 0.02 27 8.4 0.01 16 LYD518 67748.4 — — — 13.9 0.21 16 8.4 L 17 LYD518 67750.1 0.9 0.28 17 19.1 0.02 60 8.7 L 21 LYD518 67750.6 0.9 0.25 15 13.8 0.23 15 7.8 0.14  8 LYD516 67743.4 1.0 0.15 34 17.1 0.03 44 8.4 L 17 LYD516 67744.2 0.9 0.06 19 14.8 0.06 24 8.6 L 19 LYD516 67745.4 0.9 0.17 14 15.1 0.06 27 8.3 L 15 LYD514 67508.1 0.9 0.15 15 16.5 0.09 39 8.1 0.08 12 LYD514 67508.2 — — — — — — 7.8 0.10  8 LYD514 67511.4 1.0 L 30 15.3 0.09 28 8.0 0.02 11 LYD510 67828.2 1.2 L 52 17.7 L 49 8.2 0.06 13 LYD510 67829.1 1.1 L 47 16.2 0.02 36 7.9 0.07 10 LYD510 67830.6 — — — 13.8 0.11 15 8.0 0.01 10 LYD505 67502.1 1.0 L 34 14.2 0.06 19 7.8 0.15  8 LYD505 67505.2 1.0 0.14 27 15.3 L 28 8.4 L 17 LYD505 67505.3 — — — — — — 7.8 0.19  8 LYD505 67507.1 1.0 0.08 24 13.5 0.27 13 — — — LYD505 67507.2 1.0 0.05 26 14.3 0.11 20 8.0 0.12 11 LYD469 67934.3 — — — — — — 7.9 0.03  9 LYD469 67935.1 — — — 15.2 0.27 28 8.3 0.06 15 LYD469 67937.1 — — — — — — 7.6 0.22  5 LYD462 67868.3 1.2 L 58 19.7 L 65 8.6 L 19 LYD462 67870.1 1.1 L 45 16.0 0.01 34 8.3 L 15 LYD462 67871.3 1.1 0.08 38 16.0 0.05 34 8.0 0.05 10 LYD462 67872.2 1.0 L 35 17.2 L 44 8.3 L 15 LYD455 67815.1 — — — — — — 7.7 0.19  6 LYD455 67816.3 0.9 0.03 21 15.5 0.02 30 8.5 L 18 LYD455 67817.1 0.9 0.29 13 — — — — — — LYD455 67818.4 0.9 0.18 11 — — — — — — LYD455 67818.5 — — — 14.4 0.05 21 7.8 0.19  8 LYD437 67899.4 — — — — — — 7.8 0.06  9 LYD437 67900.1 — — — — — — 7.8 0.08  8 LYD437 67900.2 0.9 0.22 22 14.1 0.18 19 7.8 0.10  8 LYD437 67902.5 — — — — — — 7.8 0.22  8 LYD424 67797.2 1.1 0.02 43 15.0 0.17 26 7.8 0.13  8 LYD424 67798.5 0.9 0.13 21 — — — — — — LYD424 67799.5 0.9 0.17 12 — — — — — — LYD419 67912.4 — — — — — — 8.5 L 17 LYD419 67913.2 0.9 0.21 15 — — — — — — LYD326 67838.1 — — — — — — 8.4 L 17 LYD326 67840.1 — — — 14.0 0.08 18 8.3 L 15 LYD326 67842.3 1.0 0.08 25 — — — — — — LYD304 67803.3 0.9 0.29 13 15.3 L 28 8.3 L 15 LYD304 67806.2 1.0 L 34 14.9 0.08 25 8.0 0.07 10 CONT. — 0.8 — — 11.9 — — 7.2 — — LYD518 67748.4 — — —  9.4 0.21 34 7.5 0.11  9 LYD518 67750.1 0.6 0.19 13 11.2 0.02 60 7.9 0.01 16 LYD516 67743.4 0.9 L 60 13.3 L 89 8.1 0.02 18 LYD516 67744.1 0.7 0.29 21  9.1 0.20 29 7.7 0.07 13 LYD514 67508.1 — — —  8.8 0.06 25 7.3 0.14  7 LYD514 67508.2 0.8 0.02 37 11.6 L 64 7.6 0.02 11 LYD514 67511.2 0.8 L 46 10.9 0.02 55 — — — LYD514 67511.3 — — —  9.3 0.06 31 7.7 L 13 LYD514 67511.4 0.7 0.02 27 10.6 L 50 7.7 0.02 13 LYD510 67828.2 — — — 10.5 0.09 50 7.8 L 14 LYD510 67829.5 0.8 L 46  9.9 0.01 40 — — — LYD505 67505.3 0.9 L 58 12.0 L 70 8.0 L 17 LYD505 67507.1 0.8 0.07 41  9.9 0.07 40 — — — LYD469 67934.3 0.8 0.06 35 10.2 0.04 45 7.5 0.13  9 LYD469 67935.3 0.7 0.05 27 — — — — — — LYD469 67936.3 0.6 0.17 15 — — — — — — LYD469 67937.1 — — —  8.9 0.27 26 — — — LYD469 67937.2 0.7 0.23 18  8.7 0.22 23 — — — LYD462 67868.3 0.7 0.09 20  9.9 0.04 40 7.7 0.01 13 LYD462 67871.3 0.7 0.19 18  9.4 0.11 33 7.4 0.12  8 LYD462 67872.2 1.0 L 76 14.5 L 106  8.2 L 20 LYD455 67816.3 — — —  9.3 0.06 32 7.8 0.18 14 LYD455 67818.4 — — —  8.0 0.21 14 — — — LYD455 67818.5 0.8 0.06 44 10.9 0.09 54 — — — LYD437 67899.1 0.7 L 32 — — — — — — LYD437 67899.4 0.9 0.04 61 11.0 0.09 56 8.2 L 20 LYD437 67900.1 0.9 L 56 11.7 0.02 66 8.0 0.06 17 LYD437 67900.2 0.7 0.09 33 10.9 0.01 54 7.5 0.17  9 LYD437 67902.5 0.8 L 45 11.7 0.03 66 7.3 0.24  6 LYD424 67798.5 0.8 0.03 36  8.9 0.21 26 — — — LYD424 67798.6 0.7 0.04 34 — — — — — — LYD424 67799.5 0.9 L 56 10.8 0.06 53 — — — LYD326 67838.1 0.6 0.15 15 — — — — — — LYD326 67839.4 0.8 L 47 12.0 L 70 7.4 0.22  8 LYD326 67840.1 0.6 0.19 10  8.3 0.11 18 — — — LYD326 67842.2 0.6 0.14 13 — — — — — — LYD304 67803.1 0.6 0.27 14  9.7 0.09 38 — — — LYD304 67805.1 0.7 0.11 22 — — — — — — LYD304 67806.1 0.9 L 55 12.6 0.01 79 8.0 L 17 LYD304 67806.2 0.9 L 65 14.3 L 103  8.0 L 17 LYD304 67807.2 0.6 0.29 17  9.2 0.23 30 7.5 0.03 10 CONT. — 0.6 — —  7.0 — — 6.8 — — Table 66. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L - p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 14467). “—” = results are still unavailable.

TABLE 67 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter RGR Of Leaf RGR Of Roots RGR Of Root Area Coverage Length Gene P- % P- % P- % Name Event # Ave. Val. Incr. Ave. Val. Incr. Ave. Val Incr. LYD480 68333.4 0.1 L 60 1.4 0.04 71 — — — LYD477 68234.1 — — — — — — 0.7 0.15 17 LYD477 68234.4 0.1 0.05 56 1.2 0.18 46 — — — LYD477 68237.1 0.1 0.24 26 1.1 0.20 38 0.8 0.08 24 LYD477 68237.2 0.1 0.21 27 — — — — — — LYD470 67126.7 0.1 0.04 48 — — — — — — LYD420 68342.1 0.1 L 82 1.6 L 102  0.7 0.24 16 LYD419 67911.3 0.1 0.06 51 1.4 0.08 72 — — — LYD418 68336.1 — — — 1.2 0.16 42 0.7 0.23 15 LYD398 68037.1 — — — — — — 0.7 0.16 17 LYD398 68038.2 0.1 0.28 24 1.2 0.15 42 — — — LYD398 68038.6 — — — — — — 0.7 0.25 14 LYD377 67952.3 0.1 0.15 33 1.1 0.23 36 — — — LYD377 67952.4 0.1 0.25 26 — — — 0.7 0.22 14 LYD377 67953.3 — — — — — — 0.7 0.12 19 LYD358 68274.1 0.1 0.24 28 1.1 0.24 36 — — — LYD352 68327.3 — — — — — — 0.7 0.19 15 LYD352 68328.3 0.1 0.25 26 — — — — — — CONT. — 0.1 — — 0.8 — — 0.6 — — LYD507 67552.3 0.1 L 92 1.6 0.02 44 0.8 0.03 17 LYD507 67552.5 0.1 0.03 43 — — — — — — LYD507 67553.4 0.1 0.05 44 — — — — — — LYD487 67498.3 0.1 0.02 43 1.4 0.24 22 0.8 0.10 12 LYD487 67500.1 0.1 0.06 37 1.4 0.18 25 0.8 0.08 12 LYD473 67494.1 0.1 0.08 31 — — — — — — LYD465 67569.2 0.1 0.08 30 — — — — — — LYD461 67522.6 0.1 0.16 28 — — — — — — LYD449 67479.1 0.1 0.11 28 — — — — — — LYD449 67482.1 — — — — — — 0.8 0.11 13 LYD393 67563.1 0.1 0.03 42 1.6 0.07 39 0.8 0.11 14 LYD390 67684.2 0.1 0.30 21 — — — — — — LYD370 67666.2 0.1 0.28 20 — — — — — — LYD370 67667.1 — — — — — — 0.8 0.28  8 LYD331 67592.1 0.1 0.04 41 — — — — — — LYD331 67593.1 0.1 0.06 35 — — — — — — LYD327 67589.5 0.1 0.05 39 1.4 0.24 24 0.8 0.13 14 LYD313 67430.1 0.1 0.20 23 — — — — — — LYD313 67432.1 0.1 0.04 48 1.8 0.02 56 0.9 0.03 18 LYD294 67406.1 0.1 L 52 1.5 0.13 31 — — — LYD294 67407.4 0.1 0.06 32 — — — — — — LYD289 67461.4 0.1 0.03 43 1.5 0.09 31 0.8 0.08 12 CONT. — 0.1 — — 1.1 — — 0.7 — — LYD477 68234.1 0.1 0.03 35 1.9 0.03 39 0.8 0.13 13 LYD456 67966.3 — — — 1.6 0.20 21 — — — LYD436 68073.1 — — — — — — 0.8 0.15 12 LYD436 68075.1 — — — — — — 0.8 0.19 11 LYD377 67952.4 0.1 0.11 21 — — — — — — LYD359 67947.2 0.1 L 41 1.7 0.08 27 — — — LYD359 67947.4 0.1 0.21 19 1.6 0.27 21 — — — LYD343 67064.3 0.1 0.22 16 — — — — — — LYD343 67066.2 — — — 1.9 0.03 39 0.8 0.07 15 LYD343 67067.3 0.1 L 44 2.1 L 59 0.8 0.15 14 LYD319 67833.3 0.1 0.07 22 — — — — — — LYD295 67971.5 0.1 L 52 1.9 0.02 42 0.8 0.06 17 CONT. — 0.1 — — 1.3 — — 0.7 — — LYD507 67552.2 0.1 L 103  1.7 L 70 0.7 0.22 13 LYD507 67552.3 0.1 0.01 55 1.6 L 53 0.8 0.05 20 LYD507 67553.5 0.1 0.02 51 1.4 0.03 39 0.7 0.20 14 LYD473 67493.1 0.1 0.02 48 1.5 0.02 48 — — — LYD473 67494.1 — — — 1.3 0.19 23 — — — LYD465 67569.2 — — — 1.3 0.17 26 0.7 0.17 15 LYD461 67522.1 — — — — — — 0.7 0.25 12 LYD461 67522.2 0.1 0.28 21 1.2 0.21 23 — — — LYD393 67563.5 0.1 0.15 34 — — — — — — LYD390 67683.5 — — — 1.3 0.18 25 0.7 0.28 12 LYD390 67684.3 0.1 0.18 29 1.3 0.17 26 — — — LYD390 67686.2 0.1 0.02 48 1.5 0.01 49 — — — LYD370 67665.2 — — — 1.2 0.24 20 — — — LYD370 67666.2 0.1 L 81 1.4 0.04 39 0.7 0.28 11 LYD370 67667.1 — — — — — — 0.7 0.29 11 LYD340 67600.5 0.1 0.16 30 — — — — — — LYD340 67601.3 0.1 L 73 1.6 L 59 0.8 0.08 19 LYD331 67593.5 0.1 0.29 21 1.4 0.06 34 — — — LYD331 67594.1 — — — 1.4 0.15 36 0.7 0.22 15 LYD331 67594.3 — — — 1.2 0.26 20 — — — LYD327 67587.4 0.1 0.17 26 1.2 0.26 22 — — — LYD327 67588.1 0.1 0.08 42 1.6 0.01 59 0.8 0.08 22 LYD327 67589.5 0.1 0.02 50 1.3 0.15 27 0.7 0.26 12 LYD327 67589.6 0.1 0.04 42 1.3 0.11 30 — — — LYD313 67432.1 0.1 0.25 25 1.4 0.07 36 — — — LYD294 67407.6 — — — 1.5 0.02 49 0.7 0.28 11 CONT. — 0.1 — — 1.0 — — 0.6 — — LYD518 67748.2 — — — 1.8 0.02 27 0.8 0.01 23 LYD518 67748.4 — — — 1.6 0.20 15 0.8 0.05 18 LYD518 67750.1 0.1 0.23 18 2.3 L 60 0.8 0.01 25 LYD518 67750.6 0.1 0.25 16 1.7 0.18 17 0.8 0.04 17 LYD516 67743.4 0.1 0.05 37 2.0 L 44 0.8 0.06 18 LYD516 67744.2 0.1 0.09 22 1.8 0.05 24 0.8 0.01 24 LYD516 67745.4 0.1 0.22 17 1.8 0.03 28 0.8 0.01 22 LYD514 67508.1 0.1 0.13 21 2.0 L 41 0.8 0.21 13 LYD514 67511.4 0.1 0.02 32 1.8 0.04 26 — — — LYD510 67828.2 0.1 L 59 2.1 L 50 0.8 0.03 23 LYD510 67829.1 0.1 L 52 1.9 L 36 0.8 0.12 14 LYD510 67830.6 — — — 1.7 0.12 18 0.8 0.02 18 LYD505 67502.1 0.1 L 37 1.7 0.09 19 0.7 0.17 12 LYD505 67505.2 0.1 0.08 28 1.8 0.01 29 0.9 L 27 LYD505 67507.1 0.1 0.08 26 — — — — — — LYD505 67507.2 0.1 0.06 27 1.7 0.11 20 0.8 0.19 13 LYD469 67934.3 — — — 1.6 0.27 14 — — — LYD469 67935.1 0.1 0.26 23 1.8 0.10 28 0.8 0.04 20 LYD469 67937.1 — — — — — — 0.7 0.26  9 LYD462 67868.3 0.1 L 64 2.3 L 63 0.8 0.12 16 LYD462 67870.1 0.1 L 50 1.9 L 34 0.8 L 25 LYD462 67871.3 0.1 0.02 40 1.9 0.01 33 0.7 0.25 11 LYD462 67872.2 0.1 L 40 2.0 L 43 0.8 0.12 15 LYD455 67815.1 — — — — — — 0.7 0.17 11 LYD455 67816.3 0.1 0.06 25 1.9 0.01 31 0.9 L 27 LYD455 67817.1 0.1 0.29 14 — — — — — — LYD455 67818.4 0.1 0.27 14 — — — — — — LYD455 67818.5 — — — 1.7 0.07 21 — — — LYD437 67899.4 — — — — — — 0.7 0.23 10 LYD437 67900.1 — — — — — — 0.7 0.20 11 LYD437 67900.2 0.1 0.15 23 1.7 0.17 18 — — — LYD424 67797.2 0.1 L 51 1.8 0.06 28 0.8 0.02 22 LYD424 67798.5 0.1 0.08 25 — — — — — — LYD424 67799.5 0.1 0.25 14 — — — 0.8 0.12 15 LYD419 67912.4 — — — — — — 0.8 L 23 LYD419 67913.2 0.1 0.19 18 — — — — — — LYD326 67838.1 0.1 0.19 25 — — — 0.8 0.02 20 LYD326 67840.1 — — — 1.7 0.13 18 0.8 0.03 19 LYD326 67842.3 0.1 0.04 30 — — — — — — LYD304 67803.3 0.1 0.28 15 1.8 0.02 28 0.8 0.04 19 LYD304 67806.2 0.1 L 38 1.7 0.07 23 — — — CONT. — 0.1 — — 1.4 — — 0.7 — — LYD518 67748.4 — — — 1.1 0.07 34 — — — LYD518 67750.1 0.1 0.30 14 1.4 L 61 0.8 0.07 14 LYD516 67743.4 0.1 L 65 1.6 L 87 0.8 0.08 15 LYD516 67744.1 0.1 0.10 30 1.1 0.12 30 0.8 0.02 20 LYD516 67745.4 — — — 1.0 0.26 20 — — — LYD514 67508.1 — — — 1.1 0.13 25 — — — LYD514 67508.2 0.1 0.01 39 1.4 L 62 — — — LYD514 67511.2 0.1 L 52 1.3 L 52 — — — LYD514 67511.3 — — — 1.1 0.06 31 0.8 0.16 10 LYD514 67511.4 0.1 0.03 30 1.3 L 47 — — — LYD510 67828.2 0.1 0.22 19 1.3 0.02 46 0.8 0.14 11 LYD510 67829.5 0.1 L 54 1.2 0.02 38 — — — LYD510 67830.2 0.1 0.24 21 1.1 0.20 28 — — — LYD505 67505.3 0.1 L 70 1.5 L 70 0.8 L 21 LYD505 67507.1 0.1 L 47 1.2 0.04 37 — — — LYD469 67934.3 0.1 0.01 41 1.2 0.02 43 — — — LYD469 67935.3 0.1 0.04 32 — — — — — — LYD469 67936.3 0.1 0.13 21 — — — — — — LYD469 67937.1 — — — 1.1 0.18 25 — — — LYD469 67937.2 0.1 0.23 18 1.1 0.19 23 — — — LYD462 67868.3 0.1 0.10 23 1.2 0.03 38 0.7 0.21  9 LYD462 67871.3 0.1 0.18 21 1.1 0.06 33 — — — LYD462 67872.2 0.1 L 91 1.7 L 104  0.8 0.01 20 LYD455 67816.3 — — — 1.1 0.06 32 0.8 0.28 10 LYD455 67818.5 0.1 L 53 1.3 0.01 55 0.8 0.13 13 LYD437 67899.1 0.1 L 38 — — — — — — LYD437 67899.4 0.1 L 72 1.3 0.02 52 0.8 0.04 16 LYD437 67900.1 0.1 L 66 1.4 L 67 0.8 0.03 19 LYD437 67900.2 0.1 0.01 43 1.3 L 54 — — — LYD437 67902.5 0.1 L 55 1.4 L 66 — — — LYD424 67798.5 0.1 L 47 1.1 0.13 27 — — — LYD424 67798.6 0.1 0.01 41 — — — — — — LYD424 67799.5 0.1 L 69 1.3 L 54 — — — LYD326 67838.1 0.1 0.20 18 — — — — — — LYD326 67839.4 0.1 L 58 1.4 L 66 — — — LYD326 67840.1 0.1 0.30 13 1.0 0.21 19 0.8 0.18 10 LYD326 67842.2 0.1 0.18 18 — — — — — — LYD304 67803.1 0.1 0.13 22 1.2 0.03 39 — — — LYD304 67805.1 0.1 0.06 28 — — — — — — LYD304 67806.1 0.1 L 61 1.5 L 77 — — — LYD304 67806.2 0.1 L 75 1.7 L 101  0.8 0.10 13 LYD304 67807.2 0.1 0.14 24 1.1 0.10 31 — — — CONT. — 0.1 — — 0.9 — — 0.7 — — Table 67. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L - p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 14467). “—” = results are still unavailable.

Results from T1 Plants

The genes presented in Tables 68-70 showed a significant improvement in plant biomass and root development since they produced a higher biomass (dry and fresh weight, Table 68), a larger leaf and root biomass (leaf area, root length and root coverage) (Table 69), and a higher relative growth rate of leaf area, root coverage and root length (Table 70) when grown under normal growth conditions, compared to control plants. Plants producing larger root biomass have better possibilities to absorb larger amount of nitrogen from soil. Plants producing larger leaf biomass has better ability to produce assimilates). The genes were cloned under the regulation of a constitutive promoter (At6669; SEQ ID NO:14467). The evaluation of each gene was performed by testing the performance of different number of events. Some of the genes were evaluated in more than one tissue culture assay. This second experiment confirmed the significant increment in leaf and root performance. Event with p-value<0.1 was considered statistically significant.

Tables 68-70 summarize the observed phenotypes of transgenic plants expressing the gene constructs using the TC-T1 Assays.

TABLE 68 Genes showing improved plant performance at Normal growth conditions under regulation of A6669 promoter Dry Weight [mg] Fresh Weight [mg] Gene Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD467 11.2 0.15 20 — — — LYD427 11.0 0.17 18 176.4 0.12 24 LYD407 11.2 0.23 20 192.3 0.15 36 LYD300 10.35 0.37 11 163.7 0.27 15.5 LYD353 10.1 0.53 8.6 163.2 0.33 15.1 LYD378 9.95 0.57 6.9 179.4 0.69 5.3 LYD380 — — — 147.6 0.76 4.1 CONT. 9.3 — — 141.8 — — LYD383 11.9 0.02 35 200.5 0.06 29 CONT. 8.8 — — 156.0 — — Table 68. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L - p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 14467). “—” = results are still unavailable.

TABLE 69 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter Leaf Area Roots Coverage Roots Length Gene [cm²] [cm²] [cm] Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD467 0.8 L 17 — — — 6.7 0.09 14 LYD407 0.8 0.16 11 8.9 0.29 26 7.0 0.22 19 LYD380 — — — — — — 6.4 0.45 8.9 CONT. 0.7 — — 7.1 — — 5.9 — — LYD413 — — — 8.0 0.28 21 6.6 0.14 16 LYD383 0.9 0.04 35 — — — — — — LYD500 0.7 0.93  8 6.7 0.9    1.8 6.1 0.55 6 CONT. 0.7 — — 6.6 — — 5.7 — — Table 69. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L - p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 14467). “—” = results are still unavailable.

TABLE 70 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter RGR Of Leaf RGR Of Roots RGR Of Root Gene Area Coverage Length Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD467 0.1 0.03 20 — — — 0.7 0.10 18 LYD407 0.1 0.29 10 1.1 0.10 26 0.8 0.03 26 CONT. 0.1 — — 0.9 — — 0.6 — — LYD413 — — — 1.0 0.22 22 0.8 0.05 18 LYD383 0.1 L 45 — — — — — — CONT. 0.1 — — 0.8 — — 0.7 — — Table 70. “CONT.”—Control; “Ave.”—Average; “% Incr.” = % increment; “p-val.”—p-value, L - p < 0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 14467). “—” = results are still unavailable.

These results demonstrate that the polynucleotides of the invention are capable of improving yield and additional valuable important agricultural traits such as increase of biomass, abiotic stress tolerance, nitrogen use efficiency, yield, vigor, fiber yield and/or quality. Thus, transformed plants showing improved fresh and dry weight demonstrate the gene capacity to improve biomass a key trait of crops for forage and plant productivity; transformed plants showing improvement of seed yield demonstrate the genes capacity to improve plant productivity; transformed plants showing improvement of plot coverage and rosette diameter demonstrate the genes capacity to improve plant drought resistance as they reduce the loss of soil water by simple evaporation and reduce the competition with weeds; hence reduce the need to use herbicides to control weeds. Transformed plants showing improvement of relative growth rate of various organs (leaf and root) demonstrate the gene capacity to promote plant growth and hence shortening the needed growth period and/or alternatively improving the utilization of available nutrients and water leading to increase of land productivity; Transformed plants showing improvement of organ number as demonstrated by the leaf number parameter exhibit a potential to improve biomass yield important for forage crops and improve the plant productivity; Transformed plants showing increased root length and coverage demonstrate the gene capacity to improve drought resistance and better utilization of fertilizers as the roots can reach larger soil volume; Transformed plants showing improvement of leaf petiole relative area and leaf blade area demonstrate the genes capacity to cope with limited light intensities results from increasing the plant population densities and hence improve land productivity.

Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to those skilled in the art. Accordingly, it is intended to embrace all such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims.

All publications, patents and patent applications mentioned in this specification are herein incorporated in their entirety by reference into the specification, to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated herein by reference. In addition, citation or identification of any reference in this application shall not be construed as an admission that such reference is available as prior art to the present invention. To the extent that section headings are used, they should not be construed as necessarily limiting.

LENGTHY TABLES The patent application contains a lengthy table section. A copy of the table is available in electronic form from the USPTO web site (http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20190119695A1). An electronic copy of the table will also be available from the USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3). 

What is claimed is:
 1. A method of increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency and/or reducing time to flowering and/or time to inflorescence emergence of a plant, comprising over-expressing within the plant a polypeptide comprising an amino acid sequence at least 80% identical to SEQ ID NO: 757, 456-756, 758-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 or 14462, thereby increasing the yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency, and/or reducing the time to flowering and/or the time to inflorescence emergence of the plant.
 2. The method of claim 1, wherein said amino acid sequence is at least 90% identical to the amino acid sequence selected from the group consisting of SEQ ID NOs: 757, 456-756, 758-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 and
 14462. 3. The method of claim 1, wherein said amino acid sequence is at least 95% identical to the amino acid sequence selected from the group consisting of SEQ ID NOs: 757, 456-756, 758-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 and
 14462. 4. The method of claim 1, wherein said amino acid sequence is selected from the group consisting of SEQ ID NOs: 757, 456-756, 758-774, 8385-10836, 10838-14461 and
 14462. 5. The method of claim 1, wherein said over-expressing said polypeptide is effected by transforming a cell of the plant with an exogenous polynucleotide comprising a nucleic acid sequence encoding said polypeptide.
 6. The method of claim 4, further comprising selecting a plant over-expressing said polypeptide as compared to a native plant of the same species under the same growth conditions and having at least one trait selected from the group consisting of: increased yield, increased biomass, increased growth rate, increased oil content, increased fiber yield, increased fiber quality, increased abiotic stress tolerance, increased nitrogen use efficiency, reduced time to flowering and reduced time to inflorescence emergence as compared to said trait in a native plant of the same species under the same growth conditions.
 7. The method of claim 6, further comprising: (a) isolating regenerable portion of said plant selected according to claim 6 so as to obtain isolated regenerable portion of said selected plants; and (b) regenerating plants from said isolated regenerable portion of said selected plants, wherein plants without the said trait are not isolated and not regenerated.
 8. A nucleic acid construct comprising an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises an amino acid sequence at least 80% identical to the amino acid sequence set forth in SEQ ID NO: 757, 456-756, 758-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 or 14462 and a promoter for directing transcription of said nucleic acid sequence in a host cell, wherein said promoter is heterologous to said isolated polynucleotide, wherein said amino acid sequence is capable of increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency, and/or reducing time to flowering and/or time to inflorescence emergence of a plant.
 9. The nucleic acid construct of claim 8, wherein said amino acid sequence is at least 90% identical to the amino acid sequence selected from the group consisting of SEQ ID NOs: 757, 456-756, 758-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 and
 14462. 10. The nucleic acid construct of claim 8, wherein said amino acid sequence is at least 95% identical to the amino acid sequence selected from the group consisting of SEQ ID NOs: 757, 456-756, 758-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 and
 14462. 11. The nucleic acid construct of claim 8, wherein said amino acid sequence is selected from the group consisting of SEQ ID NOs: 757, 456-756, 758-774, 8385-10836, 10838-14461 and
 14462. 12. A plant cell comprising a nucleic acid construct comprising an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises an amino acid sequence at least 80% identical to the amino acid sequence set forth in SEQ ID NO: 757, 456-756, 758-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 or 14462 and a promoter for directing transcription of said nucleic acid sequence in a host cell, wherein said promoter is heterologous to said isolated polynucleotide and/or to said plant cell, wherein said amino acid sequence is capable of increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency, and/or reducing time to flowering and/or time to inflorescence emergence of a plant.
 13. The plant cell of claim 12, wherein said amino acid sequence is at least 90% identical to the amino acid sequence selected from the group consisting of SEQ ID NOs: 757, 456-756, 758-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 and
 14462. 14. The plant cell of claim 12, wherein said amino acid sequence is at least 95% identical to the amino acid sequence selected from the group consisting of SEQ ID NOs: 757, 456-756, 758-774, 8385-8643, 8645-10650, 10652-10836, 10838-12575, 12577, 12579-12583, 12585, 12586, 12590, 12591, 12593-12615, 12617-12624, 12628-12637, 12639-12659, 12662-12666, 12668-12677, 12679-12681, 12683-12695, 12697-12705, 12707-12709, 12711-12717, 12719-12727, 12729-12755, 12757-12811, 12813, 12815-12817, 12819-12825, 12827-12840, 12847-12848, 12850, 12853, 12855-12859, 12861-12884, 12886, 12887, 12893, 12895, 12896, 12898-12902, 12904-12912, 12916-12926, 12930-12937, 12940-12942, 12945-12954, 12956-12962, 12965-12967, 12969-12977, 12979-12984, 12986-12992, 12994, 12999-13001, 13003, 13006-13010, 13012-13016, 13018-13019, 13021-13029, 13031-13049, 13051-13054, 13056-13063, 13065-13066, 13068-13070, 13073-13076, 13079-13084, 13086-14461 and
 14462. 15. The plant cell of claim 12, wherein said amino acid sequence is selected from the group consisting of SEQ ID NOs: 757, 456-756, 758-774, 8385-10836, 10838-14461 and
 14462. 16. The method of claim 5, wherein said nucleic acid sequence is selected from the group consisting of SEQ ID NOs: 377, 1-376, 378-455, and 775-8384.
 17. The plant cell of claim 12, wherein said plant cell forms part of a plant.
 18. The method of claim 1, further comprising growing the plant expressing said exogenous polynucleotide under the abiotic stress.
 19. The method of claim 1, wherein said abiotic stress is selected from the group consisting of salinity, drought, water deprivation, flood, etiolation, low temperature, high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency, nutrient excess, atmospheric pollution and UV irradiation.
 20. A transgenic plant comprising the nucleic acid construct of claim
 8. 21. A method of generating a transgenic plant, comprising expressing the nucleic acid construct of claim 8 within the plant, thereby generating the transgenic plant.
 22. The method of claim 1, further comprising growing the plant expressing said exogenous polynucleotide under nitrogen-limiting conditions. 